diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config index 5603e2a..c6847cf 100644 --- a/conf/containers_conda_lock_files_amd64.config +++ b/conf/containers_conda_lock_files_amd64.config @@ -1,2 +1,28 @@ +process { withName: 'COUNTS_TO_FITNESS' { conda = 'modules/local/fitness/counts_to_fitness/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'DMSANALYSIS_AASEQ' { conda = 'modules/local/dmsanalysis/aa_seq/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_FALSE_DOUBLES' { conda = 'modules/local/dmsanalysis/error_correction_false_doubles/.conda-lock/linux_amd64-bd-801bac9c074a1f9b_1.txt' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_WILDTYPE' { conda = 'modules/local/dmsanalysis/error_correction_wildtype/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'DMSANALYSIS_POSSIBLE_MUTATIONS' { conda = 'modules/local/dmsanalysis/possible_mutations/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'DMSANALYSIS_PROCESS_VARIANT_COUNTS' { conda = 'modules/local/dmsanalysis/process_variant_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'EXPDESIGN_FITNESS' { conda = 'modules/local/fitness/fitness_experimental_design/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } process { withName: 'FASTQC' { conda = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-b342db7b694c9af4_1.txt' } } +process { withName: 'FASTQ_CHECK' { conda = 'modules/local/fastq_check/.conda-lock/linux_amd64-bd-b3082ff93d0ccff0_1.txt' } } +process { withName: 'FIND_SYNONYMOUS_MUTATION' { conda = 'modules/local/fitness/find_synonymous_mutation/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'FITNESS_CALCULATION' { conda = 'modules/local/fitness/fitness_calculation/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'FITNESS_HEATMAP' { conda = 'modules/local/fitness/fitness_heatmap/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'FITNESS_QC' { conda = 'modules/local/fitness/fitness_QC/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'MERGE_ALIGN' { conda = 'modules/local/bamprocessing/merge_align/.conda-lock/linux_amd64-bd-68780a2d1eaef64d_1.txt' } } +process { withName: 'MERGE_COUNTS' { conda = 'modules/local/fitness/merge_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' } } +process { withName: 'RUN_DIMSUM' { conda = 'modules/local/fitness/run_dimsum/.conda-lock/linux_amd64-bd-833765ab7b2cf9aa_1.txt' } } +process { withName: 'RUN_MUTSCAN' { conda = 'modules/local/fitness/run_mutscan/.conda-lock/linux_amd64-bd-c5cefc95c9f1002e_1.txt' } } +process { withName: 'VARIANTCOUNTING' { conda = 'modules/local/variantcounting/.conda-lock/linux_amd64-bd-f223db6b9aa476d1_1.txt' } } +process { withName: 'VARIANT_EFFECT_INSPECTION_TOOL' { conda = 'modules/local/structure/variant_effect_inspection_tool/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt' } } +process { withName: 'VISUALIZATION_COUNTS_HEATMAP' { conda = 'modules/local/visualization/counts_heatmap/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'VISUALIZATION_COUNTS_PER_COV' { conda = 'modules/local/visualization/counts_per_cov/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'VISUALIZATION_ERROR_CORRECTION_REPORT' { conda = 'modules/local/visualization/error_correction_report/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt' } } +process { withName: 'VISUALIZATION_GLOBAL_POS_BIASES_COUNTS' { conda = 'modules/local/visualization/global_pos_biases_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'VISUALIZATION_GLOBAL_POS_BIASES_COV' { conda = 'modules/local/visualization/global_pos_biases_cov/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'VISUALIZATION_LOGDIFF' { conda = 'modules/local/visualization/logdiff/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'VISUALIZATION_SEQDEPTH' { conda = 'modules/local/visualization/seqdepth/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt' } } +process { withName: 'VISUALIZATION_SUMMARY_REPORT' { conda = 'modules/local/visualization/summary_report/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt' } } diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config index aa80a6f..a7fdf07 100644 --- a/conf/containers_conda_lock_files_arm64.config +++ b/conf/containers_conda_lock_files_arm64.config @@ -1,2 +1,27 @@ +process { withName: 'COUNTS_TO_FITNESS' { conda = 'modules/local/fitness/counts_to_fitness/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'DMSANALYSIS_AASEQ' { conda = 'modules/local/dmsanalysis/aa_seq/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_FALSE_DOUBLES' { conda = 'modules/local/dmsanalysis/error_correction_false_doubles/.conda-lock/linux_arm64-bd-fbcc673012c62cb0_1.txt' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_WILDTYPE' { conda = 'modules/local/dmsanalysis/error_correction_wildtype/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'DMSANALYSIS_POSSIBLE_MUTATIONS' { conda = 'modules/local/dmsanalysis/possible_mutations/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'DMSANALYSIS_PROCESS_VARIANT_COUNTS' { conda = 'modules/local/dmsanalysis/process_variant_counts/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'EXPDESIGN_FITNESS' { conda = 'modules/local/fitness/fitness_experimental_design/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } process { withName: 'FASTQC' { conda = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-7c8a53b986d9a000_1.txt' } } +process { withName: 'FASTQ_CHECK' { conda = 'modules/local/fastq_check/.conda-lock/linux_arm64-bd-41c3b62452310f82_1.txt' } } +process { withName: 'FIND_SYNONYMOUS_MUTATION' { conda = 'modules/local/fitness/find_synonymous_mutation/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'FITNESS_CALCULATION' { conda = 'modules/local/fitness/fitness_calculation/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'FITNESS_HEATMAP' { conda = 'modules/local/fitness/fitness_heatmap/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'FITNESS_QC' { conda = 'modules/local/fitness/fitness_QC/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'MERGE_ALIGN' { conda = 'modules/local/bamprocessing/merge_align/.conda-lock/linux_arm64-bd-7b395b04348e2784_1.txt' } } +process { withName: 'MERGE_COUNTS' { conda = 'modules/local/fitness/merge_counts/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' } } +process { withName: 'RUN_DIMSUM' { conda = 'modules/local/fitness/run_dimsum/.conda-lock/linux_arm64-bd-8a66e8e1354d6370_1.txt' } } +process { withName: 'VARIANTCOUNTING' { conda = 'modules/local/variantcounting/.conda-lock/linux_arm64-bd-4cc0c5d536e48053_1.txt' } } +process { withName: 'VARIANT_EFFECT_INSPECTION_TOOL' { conda = 'modules/local/structure/variant_effect_inspection_tool/.conda-lock/linux_arm64-bd-a15c6f547e2083b8_1.txt' } } +process { withName: 'VISUALIZATION_COUNTS_HEATMAP' { conda = 'modules/local/visualization/counts_heatmap/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'VISUALIZATION_COUNTS_PER_COV' { conda = 'modules/local/visualization/counts_per_cov/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'VISUALIZATION_ERROR_CORRECTION_REPORT' { conda = 'modules/local/visualization/error_correction_report/.conda-lock/linux_arm64-bd-a15c6f547e2083b8_1.txt' } } +process { withName: 'VISUALIZATION_GLOBAL_POS_BIASES_COUNTS' { conda = 'modules/local/visualization/global_pos_biases_counts/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'VISUALIZATION_GLOBAL_POS_BIASES_COV' { conda = 'modules/local/visualization/global_pos_biases_cov/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'VISUALIZATION_LOGDIFF' { conda = 'modules/local/visualization/logdiff/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'VISUALIZATION_SEQDEPTH' { conda = 'modules/local/visualization/seqdepth/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt' } } +process { withName: 'VISUALIZATION_SUMMARY_REPORT' { conda = 'modules/local/visualization/summary_report/.conda-lock/linux_arm64-bd-a15c6f547e2083b8_1.txt' } } diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config index dbab23d..a8416f6 100644 --- a/conf/containers_docker_amd64.config +++ b/conf/containers_docker_amd64.config @@ -1,2 +1,28 @@ +process { withName: 'COUNTS_TO_FITNESS' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'DMSANALYSIS_AASEQ' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_FALSE_DOUBLES' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-stringr:801bac9c074a1f9b' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_WILDTYPE' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'DMSANALYSIS_POSSIBLE_MUTATIONS' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'DMSANALYSIS_PROCESS_VARIANT_COUNTS' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'EXPDESIGN_FITNESS' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.13.0--b342db7b694c9af4' } } +process { withName: 'FASTQ_CHECK' { container = 'community.wave.seqera.io/library/fq:0.12.0--b3082ff93d0ccff0' } } +process { withName: 'FIND_SYNONYMOUS_MUTATION' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'FITNESS_CALCULATION' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'FITNESS_HEATMAP' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'FITNESS_QC' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'MERGE_ALIGN' { container = 'community.wave.seqera.io/library/bwa_samtools_vsearch:68780a2d1eaef64d' } } +process { withName: 'MERGE_COUNTS' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc' } } +process { withName: 'RUN_DIMSUM' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-dimsum_r-base_r-data.table_pruned:cca13eed371a9d84' } } +process { withName: 'RUN_MUTSCAN' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base:c5cefc95c9f1002e' } } +process { withName: 'VARIANTCOUNTING' { container = 'community.wave.seqera.io/library/pysam_biopython_numpy_polars-lts-cpu_pruned:f223db6b9aa476d1' } } +process { withName: 'VARIANT_EFFECT_INSPECTION_TOOL' { container = 'community.wave.seqera.io/library/numpy_pandas_python:cfb38dbf0574e16d' } } +process { withName: 'VISUALIZATION_COUNTS_HEATMAP' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'VISUALIZATION_COUNTS_PER_COV' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'VISUALIZATION_ERROR_CORRECTION_REPORT' { container = 'community.wave.seqera.io/library/numpy_pandas_python:cfb38dbf0574e16d' } } +process { withName: 'VISUALIZATION_GLOBAL_POS_BIASES_COUNTS' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'VISUALIZATION_GLOBAL_POS_BIASES_COV' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'VISUALIZATION_LOGDIFF' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'VISUALIZATION_SEQDEPTH' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7' } } +process { withName: 'VISUALIZATION_SUMMARY_REPORT' { container = 'community.wave.seqera.io/library/numpy_pandas_python:cfb38dbf0574e16d' } } diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config index 2318f4d..8a8cc73 100644 --- a/conf/containers_docker_arm64.config +++ b/conf/containers_docker_arm64.config @@ -1,2 +1,26 @@ +process { withName: 'COUNTS_TO_FITNESS' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'DMSANALYSIS_AASEQ' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_FALSE_DOUBLES' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-stringr:fbcc673012c62cb0' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_WILDTYPE' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'DMSANALYSIS_POSSIBLE_MUTATIONS' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'DMSANALYSIS_PROCESS_VARIANT_COUNTS' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'EXPDESIGN_FITNESS' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.13.0--7c8a53b986d9a000' } } +process { withName: 'FASTQ_CHECK' { container = 'community.wave.seqera.io/library/fq:0.12.0--41c3b62452310f82' } } +process { withName: 'FIND_SYNONYMOUS_MUTATION' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'FITNESS_CALCULATION' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'FITNESS_HEATMAP' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'FITNESS_QC' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'MERGE_ALIGN' { container = 'community.wave.seqera.io/library/bwa_samtools_vsearch:7b395b04348e2784' } } +process { withName: 'MERGE_COUNTS' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5' } } +process { withName: 'VARIANTCOUNTING' { container = 'community.wave.seqera.io/library/pysam_biopython_numpy_polars-lts-cpu_pruned:4cc0c5d536e48053' } } +process { withName: 'VARIANT_EFFECT_INSPECTION_TOOL' { container = 'community.wave.seqera.io/library/numpy_pandas_python:a15c6f547e2083b8' } } +process { withName: 'VISUALIZATION_COUNTS_HEATMAP' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'VISUALIZATION_COUNTS_PER_COV' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'VISUALIZATION_ERROR_CORRECTION_REPORT' { container = 'community.wave.seqera.io/library/numpy_pandas_python:a15c6f547e2083b8' } } +process { withName: 'VISUALIZATION_GLOBAL_POS_BIASES_COUNTS' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'VISUALIZATION_GLOBAL_POS_BIASES_COV' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'VISUALIZATION_LOGDIFF' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'VISUALIZATION_SEQDEPTH' { container = 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb' } } +process { withName: 'VISUALIZATION_SUMMARY_REPORT' { container = 'community.wave.seqera.io/library/numpy_pandas_python:a15c6f547e2083b8' } } diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config index 094956c..02a459b 100644 --- a/conf/containers_singularity_https_amd64.config +++ b/conf/containers_singularity_https_amd64.config @@ -1,2 +1,28 @@ +process { withName: 'COUNTS_TO_FITNESS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'DMSANALYSIS_AASEQ' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_FALSE_DOUBLES' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e5/e5a2e5419dff47f9dbcea8823692f60f9a1b1c1a1ee32ae56eef0ce2989f7b72/data' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_WILDTYPE' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'DMSANALYSIS_POSSIBLE_MUTATIONS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'DMSANALYSIS_PROCESS_VARIANT_COUNTS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'EXPDESIGN_FITNESS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/81/816bda6dd014e810753f642611232443ddeabb2b47f9681ad43f9044816f00ff/data' } } +process { withName: 'FASTQ_CHECK' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1e/1edbe701f591caa7f7a930781d0364392706d291016f1028b5b9fe501ec6ef8c/data' } } +process { withName: 'FIND_SYNONYMOUS_MUTATION' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'FITNESS_CALCULATION' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'FITNESS_HEATMAP' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'FITNESS_QC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'MERGE_ALIGN' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1e/1e03db44377380bacb3a5ec57a7e77ad36603863b3f0e821d2268a47981572b1/data' } } +process { withName: 'MERGE_COUNTS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' } } +process { withName: 'RUN_DIMSUM' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/92/9298c391f285d7f2c1155f6a519a96c4f7591971780ba4f10569558282f40b6f/data' } } +process { withName: 'RUN_MUTSCAN' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0a/0a32a5f637634c064a3caecc77d9e99f4367efd459bc28d1d4971ed5d05b73a7/data' } } +process { withName: 'VARIANTCOUNTING' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/62/6247bcc77159c0adea94e0fdc439006f94d499e9d32004470fa7e402ede08538/data' } } +process { withName: 'VARIANT_EFFECT_INSPECTION_TOOL' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f727259d394cff047a26f3e3fa3a43e1a7a1c9dc51a35e6def7aa90a2085bb7b/data' } } +process { withName: 'VISUALIZATION_COUNTS_HEATMAP' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'VISUALIZATION_COUNTS_PER_COV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'VISUALIZATION_ERROR_CORRECTION_REPORT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f727259d394cff047a26f3e3fa3a43e1a7a1c9dc51a35e6def7aa90a2085bb7b/data' } } +process { withName: 'VISUALIZATION_GLOBAL_POS_BIASES_COUNTS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'VISUALIZATION_GLOBAL_POS_BIASES_COV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'VISUALIZATION_LOGDIFF' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'VISUALIZATION_SEQDEPTH' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' } } +process { withName: 'VISUALIZATION_SUMMARY_REPORT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f727259d394cff047a26f3e3fa3a43e1a7a1c9dc51a35e6def7aa90a2085bb7b/data' } } diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config index 9078182..6738b71 100644 --- a/conf/containers_singularity_https_arm64.config +++ b/conf/containers_singularity_https_arm64.config @@ -1,2 +1,26 @@ +process { withName: 'COUNTS_TO_FITNESS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'DMSANALYSIS_AASEQ' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_FALSE_DOUBLES' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cc/ccd8ca061a33803f1d15bc47bf8e6d87b242ebb66b387cbb5ab02a4c7670f425/data' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_WILDTYPE' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'DMSANALYSIS_POSSIBLE_MUTATIONS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'DMSANALYSIS_PROCESS_VARIANT_COUNTS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'EXPDESIGN_FITNESS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ad/add047b79c7b7b0f2c0711161f64256ffe51ebf8a6e14fa7adf31877da6425db/data' } } +process { withName: 'FASTQ_CHECK' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ba09e7d98be1120310df58960280440253953eaba0da00d71cd6b3f13211f9/data' } } +process { withName: 'FIND_SYNONYMOUS_MUTATION' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'FITNESS_CALCULATION' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'FITNESS_HEATMAP' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'FITNESS_QC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'MERGE_ALIGN' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6f/6f3676079712b1ee571f0a90e69b8d197fcb1ba68085cf475a25cc74bd4cb45a/data' } } +process { withName: 'MERGE_COUNTS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data' } } +process { withName: 'VARIANTCOUNTING' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/00/009b2a9e9a23d373d35a9afb3e353449f962bcc5511cb56aa3a286b942b0d514/data' } } +process { withName: 'VARIANT_EFFECT_INSPECTION_TOOL' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/22/229745e9be125462f1850ac75f13afb0738d30241558908657bfc802c2c6681f/data' } } +process { withName: 'VISUALIZATION_COUNTS_HEATMAP' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'VISUALIZATION_COUNTS_PER_COV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'VISUALIZATION_ERROR_CORRECTION_REPORT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/22/229745e9be125462f1850ac75f13afb0738d30241558908657bfc802c2c6681f/data' } } +process { withName: 'VISUALIZATION_GLOBAL_POS_BIASES_COUNTS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'VISUALIZATION_GLOBAL_POS_BIASES_COV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'VISUALIZATION_LOGDIFF' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'VISUALIZATION_SEQDEPTH' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data' } } +process { withName: 'VISUALIZATION_SUMMARY_REPORT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/22/229745e9be125462f1850ac75f13afb0738d30241558908657bfc802c2c6681f/data' } } diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config index 7851f30..e45ca59 100644 --- a/conf/containers_singularity_oras_amd64.config +++ b/conf/containers_singularity_oras_amd64.config @@ -1,2 +1,27 @@ +process { withName: 'COUNTS_TO_FITNESS' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'DMSANALYSIS_AASEQ' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_FALSE_DOUBLES' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-stringr:f7ed82e8081ab38d' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_WILDTYPE' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'DMSANALYSIS_POSSIBLE_MUTATIONS' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'DMSANALYSIS_PROCESS_VARIANT_COUNTS' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'EXPDESIGN_FITNESS' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.13.0--aadddbed09923ea6' } } +process { withName: 'FASTQ_CHECK' { container = 'oras://community.wave.seqera.io/library/fq:0.12.0--2eebf4e58a46525e' } } +process { withName: 'FIND_SYNONYMOUS_MUTATION' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'FITNESS_CALCULATION' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'FITNESS_HEATMAP' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'FITNESS_QC' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'MERGE_ALIGN' { container = 'oras://community.wave.seqera.io/library/bwa_samtools_vsearch:22b018a8e6d18e4f' } } +process { withName: 'MERGE_COUNTS' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2' } } +process { withName: 'RUN_MUTSCAN' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base:764a8471b126fb35' } } +process { withName: 'VARIANTCOUNTING' { container = 'oras://community.wave.seqera.io/library/pysam_biopython_numpy_polars-lts-cpu_pruned:52b881e1947dfdb0' } } +process { withName: 'VARIANT_EFFECT_INSPECTION_TOOL' { container = 'oras://community.wave.seqera.io/library/numpy_pandas_python:7f16bcac97973062' } } +process { withName: 'VISUALIZATION_COUNTS_HEATMAP' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'VISUALIZATION_COUNTS_PER_COV' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'VISUALIZATION_ERROR_CORRECTION_REPORT' { container = 'oras://community.wave.seqera.io/library/numpy_pandas_python:7f16bcac97973062' } } +process { withName: 'VISUALIZATION_GLOBAL_POS_BIASES_COUNTS' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'VISUALIZATION_GLOBAL_POS_BIASES_COV' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'VISUALIZATION_LOGDIFF' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'VISUALIZATION_SEQDEPTH' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb' } } +process { withName: 'VISUALIZATION_SUMMARY_REPORT' { container = 'oras://community.wave.seqera.io/library/numpy_pandas_python:7f16bcac97973062' } } diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config index 0b561a1..09983ca 100644 --- a/conf/containers_singularity_oras_arm64.config +++ b/conf/containers_singularity_oras_arm64.config @@ -1,2 +1,26 @@ +process { withName: 'COUNTS_TO_FITNESS' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7' } } +process { withName: 'DMSANALYSIS_AASEQ' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_FALSE_DOUBLES' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-stringr:1c3d5150b5f34345' } } +process { withName: 'DMSANALYSIS_ERROR_CORRECTION_WILDTYPE' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7' } } +process { withName: 'DMSANALYSIS_POSSIBLE_MUTATIONS' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7' } } +process { withName: 'DMSANALYSIS_PROCESS_VARIANT_COUNTS' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7' } } +process { withName: 'EXPDESIGN_FITNESS' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7' } } process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.13.0--f5a404ab2c13e090' } } +process { withName: 'FASTQ_CHECK' { container = 'oras://community.wave.seqera.io/library/fq:0.12.0--8bfef4392e820de8' } } +process { withName: 'FIND_SYNONYMOUS_MUTATION' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7' } } +process { withName: 'FITNESS_CALCULATION' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7' } } +process { withName: 'FITNESS_HEATMAP' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7' } } +process { withName: 'FITNESS_QC' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7' } } +process { withName: 'MERGE_ALIGN' { container = 'oras://community.wave.seqera.io/library/bwa_samtools_vsearch:a79e451fc67cfde0' } } +process { withName: 'MERGE_COUNTS' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7' } } process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81' } } +process { withName: 'VARIANTCOUNTING' { container = 'oras://community.wave.seqera.io/library/pysam_biopython_numpy_polars-lts-cpu_pruned:9df342605773fef4' } } +process { withName: 'VARIANT_EFFECT_INSPECTION_TOOL' { container = 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+process { withName: 'VISUALIZATION_LOGDIFF' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7' } } +process { withName: 'VISUALIZATION_SEQDEPTH' { container = 'oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7' } } +process { withName: 'VISUALIZATION_SUMMARY_REPORT' { container = 'oras://community.wave.seqera.io/library/numpy_pandas_python:648dc1860698d21b' } } diff --git a/docs/usage.md b/docs/usage.md index 2167883..9fe4ad3 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -197,7 +197,9 @@ Two established statistical frameworks can be run on the same merged counts: } ``` -- `--mutscan`: [mutscan](https://github.com/fmicompbio/mutscan) enrichment estimates with edgeR and limma, on the same merged count table. + DiMSum's container is currently only available for x86-64 (amd64), so on ARM machines (e.g. Apple Silicon) `--dimsum` runs under amd64 emulation, and the `arm64` profile has no native image for it. + +- `--mutscan`: [mutscan](https://github.com/fmicompbio/mutscan) enrichment estimates with edgeR and limma, on the same merged count table. mutscan is currently only packaged for x86-64 (amd64), so on ARM machines (e.g. Apple Silicon) `--mutscan` runs under amd64 emulation, and the `arm64` profile has no native image for it. ### Interactive variant effect inspection tool (`--pdb`) diff --git a/modules/local/bamprocessing/merge_align/.conda-lock/linux_amd64-bd-68780a2d1eaef64d_1.txt b/modules/local/bamprocessing/merge_align/.conda-lock/linux_amd64-bd-68780a2d1eaef64d_1.txt new file mode 100644 index 0000000..703ea92 --- /dev/null +++ b/modules/local/bamprocessing/merge_align/.conda-lock/linux_amd64-bd-68780a2d1eaef64d_1.txt @@ -0,0 +1,397 @@ +version: 6 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + - url: https://conda.anaconda.org/bioconda/ + - url: 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/85/856173edaf176a724c7e5fe23987e42e5ab0bc476d20e458bf2a68d738e74293/data' - : 'community.wave.seqera.io/library/bwa_samtools_vsearch:593a959d25ab8798' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1e/1e03db44377380bacb3a5ec57a7e77ad36603863b3f0e821d2268a47981572b1/data' + : 'community.wave.seqera.io/library/bwa_samtools_vsearch:68780a2d1eaef64d'}" input: tuple val(meta), path(reads) diff --git a/modules/local/bamprocessing/merge_align/meta.yml b/modules/local/bamprocessing/merge_align/meta.yml index 1daf7f5..1e2e1e2 100644 --- a/modules/local/bamprocessing/merge_align/meta.yml +++ b/modules/local/bamprocessing/merge_align/meta.yml @@ -104,3 +104,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/bwa_samtools_vsearch:7b395b04348e2784 + build_id: bd-7b395b04348e2784_1 + scan_id: sc-e65dd0586cbc897a_1 + linux/amd64: + name: community.wave.seqera.io/library/bwa_samtools_vsearch:68780a2d1eaef64d + build_id: bd-68780a2d1eaef64d_1 + scan_id: sc-698b2de0eed7923f_1 + singularity: + linux/arm64: + name: oras://community.wave.seqera.io/library/bwa_samtools_vsearch:a79e451fc67cfde0 + build_id: bd-a79e451fc67cfde0_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6f/6f3676079712b1ee571f0a90e69b8d197fcb1ba68085cf475a25cc74bd4cb45a/data + linux/amd64: + name: oras://community.wave.seqera.io/library/bwa_samtools_vsearch:22b018a8e6d18e4f + build_id: bd-22b018a8e6d18e4f_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1e/1e03db44377380bacb3a5ec57a7e77ad36603863b3f0e821d2268a47981572b1/data + conda: + linux/amd64: + lock_file: modules/local/bamprocessing/merge_align/.conda-lock/linux_amd64-bd-68780a2d1eaef64d_1.txt + linux/arm64: + lock_file: modules/local/bamprocessing/merge_align/.conda-lock/linux_arm64-bd-7b395b04348e2784_1.txt diff --git a/modules/local/dmsanalysis/aa_seq/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/dmsanalysis/aa_seq/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/dmsanalysis/aa_seq/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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libzlib >=1.3.2,<2.0a0 + license: BSD-3-Clause + license_family: BSD + size: 615477 + timestamp: 1786599613561 diff --git a/modules/local/dmsanalysis/aa_seq/main.nf b/modules/local/dmsanalysis/aa_seq/main.nf index d7f462e..ad20999 100644 --- a/modules/local/dmsanalysis/aa_seq/main.nf +++ b/modules/local/dmsanalysis/aa_seq/main.nf @@ -4,9 +4,9 @@ process DMSANALYSIS_AASEQ { conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(meta), path(wt_seq) diff --git a/modules/local/dmsanalysis/aa_seq/meta.yml b/modules/local/dmsanalysis/aa_seq/meta.yml index 8c26ee5..7f6a023 100644 --- a/modules/local/dmsanalysis/aa_seq/meta.yml +++ b/modules/local/dmsanalysis/aa_seq/meta.yml @@ -46,3 +46,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + singularity: + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + conda: + linux/amd64: + lock_file: modules/local/dmsanalysis/aa_seq/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/dmsanalysis/aa_seq/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/dmsanalysis/error_correction_false_doubles/.conda-lock/linux_amd64-bd-801bac9c074a1f9b_1.txt b/modules/local/dmsanalysis/error_correction_false_doubles/.conda-lock/linux_amd64-bd-801bac9c074a1f9b_1.txt new file mode 100644 index 0000000..8f8a4a5 --- /dev/null +++ b/modules/local/dmsanalysis/error_correction_false_doubles/.conda-lock/linux_amd64-bd-801bac9c074a1f9b_1.txt @@ -0,0 +1,1399 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bc/bcd9a556c2ee2e9ce6d21749b6a15954d2578c6d4738e1ab72ea5de148ab2ab9/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-stringr:b64d48973b58dc0c' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e5/e5a2e5419dff47f9dbcea8823692f60f9a1b1c1a1ee32ae56eef0ce2989f7b72/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-stringr:801bac9c074a1f9b'}" input: tuple val(meta), path(raw_counts), path(filtered), path(completed) diff --git a/modules/local/dmsanalysis/error_correction_false_doubles/meta.yml b/modules/local/dmsanalysis/error_correction_false_doubles/meta.yml index 15e420b..780956f 100644 --- a/modules/local/dmsanalysis/error_correction_false_doubles/meta.yml +++ b/modules/local/dmsanalysis/error_correction_false_doubles/meta.yml @@ -79,3 +79,27 @@ authors: - "@MaximilianStammnitz" maintainers: - "@BenjaminWehnert1008" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-stringr:801bac9c074a1f9b + build_id: bd-801bac9c074a1f9b_1 + scan_id: sc-bb0508c32fbdbbf3_1 + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-stringr:fbcc673012c62cb0 + build_id: bd-fbcc673012c62cb0_1 + scan_id: sc-c0377bfc5c678ddc_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-stringr:f7ed82e8081ab38d + build_id: bd-f7ed82e8081ab38d_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e5/e5a2e5419dff47f9dbcea8823692f60f9a1b1c1a1ee32ae56eef0ce2989f7b72/data + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-stringr:1c3d5150b5f34345 + build_id: bd-1c3d5150b5f34345_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cc/ccd8ca061a33803f1d15bc47bf8e6d87b242ebb66b387cbb5ab02a4c7670f425/data + conda: + linux/amd64: + lock_file: modules/local/dmsanalysis/error_correction_false_doubles/.conda-lock/linux_amd64-bd-801bac9c074a1f9b_1.txt + linux/arm64: + lock_file: modules/local/dmsanalysis/error_correction_false_doubles/.conda-lock/linux_arm64-bd-fbcc673012c62cb0_1.txt diff --git a/modules/local/dmsanalysis/error_correction_wildtype/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/dmsanalysis/error_correction_wildtype/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/dmsanalysis/error_correction_wildtype/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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libzlib >=1.3.2,<2.0a0 + license: BSD-3-Clause + license_family: BSD + size: 615477 + timestamp: 1786599613561 diff --git a/modules/local/dmsanalysis/error_correction_wildtype/main.nf b/modules/local/dmsanalysis/error_correction_wildtype/main.nf index c2d449b..138286e 100644 --- a/modules/local/dmsanalysis/error_correction_wildtype/main.nf +++ b/modules/local/dmsanalysis/error_correction_wildtype/main.nf @@ -4,9 +4,9 @@ process DMSANALYSIS_ERROR_CORRECTION_WILDTYPE { conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(meta), path(filtered, stageAs: 'input_counts.csv'), path(wt_counts, stageAs: 'wildtype_counts.csv'), path(completed) diff --git a/modules/local/dmsanalysis/error_correction_wildtype/meta.yml b/modules/local/dmsanalysis/error_correction_wildtype/meta.yml index c90e73c..08c023d 100644 --- a/modules/local/dmsanalysis/error_correction_wildtype/meta.yml +++ b/modules/local/dmsanalysis/error_correction_wildtype/meta.yml @@ -61,3 +61,27 @@ authors: - "@MaximilianStammnitz" maintainers: - "@BenjaminWehnert1008" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + conda: + linux/amd64: + lock_file: modules/local/dmsanalysis/error_correction_wildtype/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/dmsanalysis/error_correction_wildtype/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/dmsanalysis/possible_mutations/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/dmsanalysis/possible_mutations/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/dmsanalysis/possible_mutations/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(meta), path(wt_seq) diff --git a/modules/local/dmsanalysis/possible_mutations/meta.yml b/modules/local/dmsanalysis/possible_mutations/meta.yml index c3944b0..03424e7 100644 --- a/modules/local/dmsanalysis/possible_mutations/meta.yml +++ b/modules/local/dmsanalysis/possible_mutations/meta.yml @@ -9,8 +9,7 @@ keywords: - mutagenesis - library design - variants -tools: - +tools: null input: - - meta: type: map @@ -54,3 +53,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + conda: + linux/amd64: + lock_file: modules/local/dmsanalysis/possible_mutations/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/dmsanalysis/possible_mutations/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/dmsanalysis/process_variant_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/dmsanalysis/process_variant_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/dmsanalysis/process_variant_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(meta), path(variantCounts) diff --git a/modules/local/dmsanalysis/process_variant_counts/meta.yml b/modules/local/dmsanalysis/process_variant_counts/meta.yml index 8ca6d4a..cae424c 100644 --- a/modules/local/dmsanalysis/process_variant_counts/meta.yml +++ b/modules/local/dmsanalysis/process_variant_counts/meta.yml @@ -5,8 +5,7 @@ keywords: - variant counting - variant filtering - dms -tools: - +tools: null input: - - meta: type: map @@ -57,3 +56,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + conda: + linux/amd64: + lock_file: modules/local/dmsanalysis/process_variant_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/dmsanalysis/process_variant_counts/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/fastq_check/.conda-lock/linux_amd64-bd-b3082ff93d0ccff0_1.txt b/modules/local/fastq_check/.conda-lock/linux_amd64-bd-b3082ff93d0ccff0_1.txt new file mode 100644 index 0000000..1443ea2 --- /dev/null +++ b/modules/local/fastq_check/.conda-lock/linux_amd64-bd-b3082ff93d0ccff0_1.txt @@ -0,0 +1,109 @@ +version: 6 +environments: + default: + channels: + - 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libstdcxx >=14 + - libgcc >=14 + license: GPL-3.0-only + license_family: GPL + size: 40249 + timestamp: 1779439555623 diff --git a/modules/local/fastq_check/main.nf b/modules/local/fastq_check/main.nf index 609dbf6..b5050eb 100644 --- a/modules/local/fastq_check/main.nf +++ b/modules/local/fastq_check/main.nf @@ -3,9 +3,9 @@ process FASTQ_CHECK { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fq:0.12.0--h9ee0642_0': - 'quay.io/biocontainers/fq:0.12.0--h9ee0642_0' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1e/1edbe701f591caa7f7a930781d0364392706d291016f1028b5b9fe501ec6ef8c/data' + : 'community.wave.seqera.io/library/fq:0.12.0--b3082ff93d0ccff0'}" input: tuple val(meta), path(reads, arity: '2') diff --git a/modules/local/fastq_check/meta.yml b/modules/local/fastq_check/meta.yml index 8920129..d96f240 100644 --- a/modules/local/fastq_check/meta.yml +++ b/modules/local/fastq_check/meta.yml @@ -48,3 +48,27 @@ output: authors: - "@MaximilianStammnitz" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/fq:0.12.0--b3082ff93d0ccff0 + build_id: bd-b3082ff93d0ccff0_1 + scan_id: sc-f21a88680f9cdf16_1 + linux/arm64: + name: community.wave.seqera.io/library/fq:0.12.0--41c3b62452310f82 + build_id: bd-41c3b62452310f82_1 + scan_id: sc-55cb6598f426fae1_1 + singularity: + linux/arm64: + name: oras://community.wave.seqera.io/library/fq:0.12.0--8bfef4392e820de8 + build_id: bd-8bfef4392e820de8_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ba09e7d98be1120310df58960280440253953eaba0da00d71cd6b3f13211f9/data + linux/amd64: + name: oras://community.wave.seqera.io/library/fq:0.12.0--2eebf4e58a46525e + build_id: bd-2eebf4e58a46525e_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1e/1edbe701f591caa7f7a930781d0364392706d291016f1028b5b9fe501ec6ef8c/data + conda: + linux/amd64: + lock_file: modules/local/fastq_check/.conda-lock/linux_amd64-bd-b3082ff93d0ccff0_1.txt + linux/arm64: + lock_file: modules/local/fastq_check/.conda-lock/linux_arm64-bd-41c3b62452310f82_1.txt diff --git a/modules/local/fitness/counts_to_fitness/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/fitness/counts_to_fitness/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/fitness/counts_to_fitness/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(meta), path(variantCounts_filtered_by_library) diff --git a/modules/local/fitness/counts_to_fitness/meta.yml b/modules/local/fitness/counts_to_fitness/meta.yml index ddf9610..9c100f4 100644 --- a/modules/local/fitness/counts_to_fitness/meta.yml +++ b/modules/local/fitness/counts_to_fitness/meta.yml @@ -48,3 +48,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + conda: + linux/amd64: + lock_file: modules/local/fitness/counts_to_fitness/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/fitness/counts_to_fitness/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/fitness/find_synonymous_mutation/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/fitness/find_synonymous_mutation/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/fitness/find_synonymous_mutation/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(sample), path(counts_merged) // from MERGE_COUNTS.out.merged_counts diff --git a/modules/local/fitness/find_synonymous_mutation/meta.yml b/modules/local/fitness/find_synonymous_mutation/meta.yml index 8b6bca2..4e6de93 100644 --- a/modules/local/fitness/find_synonymous_mutation/meta.yml +++ b/modules/local/fitness/find_synonymous_mutation/meta.yml @@ -49,3 +49,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + conda: + linux/amd64: + lock_file: modules/local/fitness/find_synonymous_mutation/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/fitness/find_synonymous_mutation/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/fitness/fitness_QC/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/fitness/fitness_QC/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/fitness/fitness_QC/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(sample), path(fitness_estimation_tsv) // from FITNESS_CALCULATION diff --git a/modules/local/fitness/fitness_QC/meta.yml b/modules/local/fitness/fitness_QC/meta.yml index 912ee6f..5cfb2ff 100644 --- a/modules/local/fitness/fitness_QC/meta.yml +++ b/modules/local/fitness/fitness_QC/meta.yml @@ -6,8 +6,7 @@ keywords: - quality control - correlation - fitness -tools: - +tools: null input: - - sample: type: map @@ -45,3 +44,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + conda: + linux/amd64: + lock_file: modules/local/fitness/fitness_QC/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/fitness/fitness_QC/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/fitness/fitness_calculation/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/fitness/fitness_calculation/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/fitness/fitness_calculation/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(sample), path(counts_merged) diff --git a/modules/local/fitness/fitness_calculation/meta.yml b/modules/local/fitness/fitness_calculation/meta.yml index b3a4fcc..19bcf0b 100644 --- a/modules/local/fitness/fitness_calculation/meta.yml +++ b/modules/local/fitness/fitness_calculation/meta.yml @@ -6,8 +6,7 @@ keywords: - fitness calculation - log-ratio - enrichment -tools: - +tools: null input: - - sample: type: map @@ -51,3 +50,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + singularity: + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + conda: + linux/amd64: + lock_file: modules/local/fitness/fitness_calculation/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/fitness/fitness_calculation/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/fitness/fitness_experimental_design/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/fitness/fitness_experimental_design/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/fitness/fitness_experimental_design/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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libzlib >=1.3.2,<2.0a0 + license: BSD-3-Clause + license_family: BSD + size: 615477 + timestamp: 1786599613561 diff --git a/modules/local/fitness/fitness_experimental_design/main.nf b/modules/local/fitness/fitness_experimental_design/main.nf index ef6e9ba..97a21fd 100644 --- a/modules/local/fitness/fitness_experimental_design/main.nf +++ b/modules/local/fitness/fitness_experimental_design/main.nf @@ -4,9 +4,9 @@ process EXPDESIGN_FITNESS { conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: path samplesheet_csv diff --git a/modules/local/fitness/fitness_experimental_design/meta.yml b/modules/local/fitness/fitness_experimental_design/meta.yml index c6c3631..a8a606d 100644 --- a/modules/local/fitness/fitness_experimental_design/meta.yml +++ b/modules/local/fitness/fitness_experimental_design/meta.yml @@ -34,3 +34,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + conda: + linux/amd64: + lock_file: modules/local/fitness/fitness_experimental_design/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/fitness/fitness_experimental_design/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/fitness/fitness_heatmap/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/fitness/fitness_heatmap/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/fitness/fitness_heatmap/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(sample), path(fitness_estimation_tsv) // from FITNESS_CALCULATION diff --git a/modules/local/fitness/fitness_heatmap/meta.yml b/modules/local/fitness/fitness_heatmap/meta.yml index 2fcf483..1de711c 100644 --- a/modules/local/fitness/fitness_heatmap/meta.yml +++ b/modules/local/fitness/fitness_heatmap/meta.yml @@ -50,3 +50,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + conda: + linux/amd64: + lock_file: modules/local/fitness/fitness_heatmap/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/fitness/fitness_heatmap/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/fitness/merge_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/fitness/merge_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/fitness/merge_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(sample), path(input_counts), path(output_counts) diff --git a/modules/local/fitness/merge_counts/meta.yml b/modules/local/fitness/merge_counts/meta.yml index fb96312..2a84b75 100644 --- a/modules/local/fitness/merge_counts/meta.yml +++ b/modules/local/fitness/merge_counts/meta.yml @@ -6,8 +6,7 @@ keywords: - count merging - variant table - preprocessing -tools: - +tools: null input: - - sample: type: map @@ -39,3 +38,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + conda: + linux/amd64: + lock_file: modules/local/fitness/merge_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/fitness/merge_counts/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/fitness/run_dimsum/.conda-lock/linux_amd64-bd-833765ab7b2cf9aa_1.txt b/modules/local/fitness/run_dimsum/.conda-lock/linux_amd64-bd-833765ab7b2cf9aa_1.txt new file mode 100644 index 0000000..51a9bf7 --- /dev/null +++ b/modules/local/fitness/run_dimsum/.conda-lock/linux_amd64-bd-833765ab7b2cf9aa_1.txt @@ -0,0 +1,3783 @@ +version: 6 +environments: + default: + channels: + - 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The conda lock files are kept from the new build. + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-dimsum_r-base_r-data.table_pruned:cca13eed371a9d84 + singularity: + linux/amd64: + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/92/9298c391f285d7f2c1155f6a519a96c4f7591971780ba4f10569558282f40b6f/data + conda: + linux/amd64: + lock_file: modules/local/fitness/run_dimsum/.conda-lock/linux_amd64-bd-833765ab7b2cf9aa_1.txt + linux/arm64: + lock_file: modules/local/fitness/run_dimsum/.conda-lock/linux_arm64-bd-8a66e8e1354d6370_1.txt diff --git a/modules/local/fitness/run_mutscan/.conda-lock/linux_amd64-bd-c5cefc95c9f1002e_1.txt b/modules/local/fitness/run_mutscan/.conda-lock/linux_amd64-bd-c5cefc95c9f1002e_1.txt new file mode 100644 index 0000000..4276d2e --- /dev/null +++ b/modules/local/fitness/run_mutscan/.conda-lock/linux_amd64-bd-c5cefc95c9f1002e_1.txt @@ -0,0 +1,3043 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f3/f380349424bfa454e3eeffd949426a422653d49a7ac7247cbf23f83e117ceb8a/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base:4e27e7b9cc2d9218' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0a/0a32a5f637634c064a3caecc77d9e99f4367efd459bc28d1d4971ed5d05b73a7/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base:c5cefc95c9f1002e'}" input: tuple val(sample), path(counts_merged) diff --git a/modules/local/fitness/run_mutscan/meta.yml b/modules/local/fitness/run_mutscan/meta.yml index 635ef03..e5319aa 100644 --- a/modules/local/fitness/run_mutscan/meta.yml +++ b/modules/local/fitness/run_mutscan/meta.yml @@ -82,3 +82,17 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base:c5cefc95c9f1002e + build_id: bd-c5cefc95c9f1002e_1 + scan_id: sc-8d031d70a3f2734f_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base:764a8471b126fb35 + build_id: bd-764a8471b126fb35_2 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0a/0a32a5f637634c064a3caecc77d9e99f4367efd459bc28d1d4971ed5d05b73a7/data + conda: + linux/amd64: + lock_file: modules/local/fitness/run_mutscan/.conda-lock/linux_amd64-bd-c5cefc95c9f1002e_1.txt diff --git a/modules/local/structure/variant_effect_inspection_tool/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt b/modules/local/structure/variant_effect_inspection_tool/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt new file mode 100644 index 0000000..e3629c8 --- /dev/null +++ b/modules/local/structure/variant_effect_inspection_tool/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt @@ -0,0 +1,556 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/97/977734114fdf9ecc0fbe96d3b2f09901eb1c4490de64d863a18679d926a028c4/data' - : 'community.wave.seqera.io/library/numpy_pandas_python:43a80707feb1fac3' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f727259d394cff047a26f3e3fa3a43e1a7a1c9dc51a35e6def7aa90a2085bb7b/data' + : 'community.wave.seqera.io/library/numpy_pandas_python:cfb38dbf0574e16d'}" input: tuple val(meta), path(pdb), path(fitness_tsv) diff --git a/modules/local/structure/variant_effect_inspection_tool/meta.yml b/modules/local/structure/variant_effect_inspection_tool/meta.yml index 5582e00..be5d948 100644 --- a/modules/local/structure/variant_effect_inspection_tool/meta.yml +++ b/modules/local/structure/variant_effect_inspection_tool/meta.yml @@ -73,3 +73,27 @@ authors: - "@BenjaminWehnert1008" maintainers: - "@BenjaminWehnert1008" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/numpy_pandas_python:cfb38dbf0574e16d + build_id: bd-cfb38dbf0574e16d_1 + scan_id: sc-fae0cdb4b6c51968_1 + linux/arm64: + name: community.wave.seqera.io/library/numpy_pandas_python:a15c6f547e2083b8 + build_id: bd-a15c6f547e2083b8_1 + scan_id: sc-931239170a8e2353_1 + singularity: + linux/arm64: + name: oras://community.wave.seqera.io/library/numpy_pandas_python:648dc1860698d21b + build_id: bd-648dc1860698d21b_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/22/229745e9be125462f1850ac75f13afb0738d30241558908657bfc802c2c6681f/data + linux/amd64: + name: oras://community.wave.seqera.io/library/numpy_pandas_python:7f16bcac97973062 + build_id: bd-7f16bcac97973062_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f727259d394cff047a26f3e3fa3a43e1a7a1c9dc51a35e6def7aa90a2085bb7b/data + conda: + linux/amd64: + lock_file: modules/local/structure/variant_effect_inspection_tool/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt + linux/arm64: + lock_file: modules/local/structure/variant_effect_inspection_tool/.conda-lock/linux_arm64-bd-a15c6f547e2083b8_1.txt diff --git a/modules/local/variantcounting/.conda-lock/linux_amd64-bd-f223db6b9aa476d1_1.txt b/modules/local/variantcounting/.conda-lock/linux_amd64-bd-f223db6b9aa476d1_1.txt new file mode 100644 index 0000000..d770317 --- /dev/null +++ b/modules/local/variantcounting/.conda-lock/linux_amd64-bd-f223db6b9aa476d1_1.txt @@ -0,0 +1,1493 @@ +version: 6 +environments: + default: + channels: + - 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container "${ workflow.containerEngine == 'singularity' - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/19/199686bb01fc18539d6ca35597ce574329a29ccae5f0b4bb1a6982f2bd3ce19a/data' - : 'community.wave.seqera.io/library/pysam_biopython_numpy_polars-lts-cpu_pruned:ac0353fd8d903112' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/62/6247bcc77159c0adea94e0fdc439006f94d499e9d32004470fa7e402ede08538/data' + : 'community.wave.seqera.io/library/pysam_biopython_numpy_polars-lts-cpu_pruned:f223db6b9aa476d1'}" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/local/variantcounting/meta.yml b/modules/local/variantcounting/meta.yml index 76d8d50..4688b2b 100644 --- a/modules/local/variantcounting/meta.yml +++ b/modules/local/variantcounting/meta.yml @@ -69,3 +69,27 @@ authors: - "@BenjaminWehnert1008" maintainers: - "@BenjaminWehnert1008" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/pysam_biopython_numpy_polars-lts-cpu_pruned:f223db6b9aa476d1 + build_id: bd-f223db6b9aa476d1_1 + scan_id: sc-7694d04e5969b2e6_1 + linux/arm64: + name: community.wave.seqera.io/library/pysam_biopython_numpy_polars-lts-cpu_pruned:4cc0c5d536e48053 + build_id: bd-4cc0c5d536e48053_1 + scan_id: sc-555693b2cbde3457_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/pysam_biopython_numpy_polars-lts-cpu_pruned:52b881e1947dfdb0 + build_id: bd-52b881e1947dfdb0_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/62/6247bcc77159c0adea94e0fdc439006f94d499e9d32004470fa7e402ede08538/data + linux/arm64: + name: oras://community.wave.seqera.io/library/pysam_biopython_numpy_polars-lts-cpu_pruned:9df342605773fef4 + build_id: bd-9df342605773fef4_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/00/009b2a9e9a23d373d35a9afb3e353449f962bcc5511cb56aa3a286b942b0d514/data + conda: + linux/amd64: + lock_file: modules/local/variantcounting/.conda-lock/linux_amd64-bd-f223db6b9aa476d1_1.txt + linux/arm64: + lock_file: modules/local/variantcounting/.conda-lock/linux_arm64-bd-4cc0c5d536e48053_1.txt diff --git a/modules/local/visualization/counts_heatmap/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/visualization/counts_heatmap/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/visualization/counts_heatmap/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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libzlib >=1.3.2,<2.0a0 + license: BSD-3-Clause + license_family: BSD + size: 615477 + timestamp: 1786599613561 diff --git a/modules/local/visualization/counts_heatmap/main.nf b/modules/local/visualization/counts_heatmap/main.nf index e4784ff..09c9eaf 100644 --- a/modules/local/visualization/counts_heatmap/main.nf +++ b/modules/local/visualization/counts_heatmap/main.nf @@ -4,9 +4,9 @@ process VISUALIZATION_COUNTS_HEATMAP { conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(meta), path(variantCounts_for_heatmaps) diff --git a/modules/local/visualization/counts_heatmap/meta.yml b/modules/local/visualization/counts_heatmap/meta.yml index f8a3c3b..5a5181e 100644 --- a/modules/local/visualization/counts_heatmap/meta.yml +++ b/modules/local/visualization/counts_heatmap/meta.yml @@ -6,8 +6,7 @@ keywords: - visualization - heatmap - mutation landscape -tools: - +tools: null input: - - meta: type: map @@ -39,3 +38,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + conda: + linux/amd64: + lock_file: modules/local/visualization/counts_heatmap/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/visualization/counts_heatmap/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/visualization/counts_per_cov/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/visualization/counts_per_cov/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/visualization/counts_per_cov/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(meta), path(variantCounts_for_heatmaps) diff --git a/modules/local/visualization/counts_per_cov/meta.yml b/modules/local/visualization/counts_per_cov/meta.yml index 5cbf126..59873e5 100644 --- a/modules/local/visualization/counts_per_cov/meta.yml +++ b/modules/local/visualization/counts_per_cov/meta.yml @@ -44,3 +44,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + singularity: + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + conda: + linux/amd64: + lock_file: modules/local/visualization/counts_per_cov/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/visualization/counts_per_cov/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/visualization/error_correction_report/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt b/modules/local/visualization/error_correction_report/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt new file mode 100644 index 0000000..e3629c8 --- /dev/null +++ b/modules/local/visualization/error_correction_report/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt @@ -0,0 +1,556 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/97/977734114fdf9ecc0fbe96d3b2f09901eb1c4490de64d863a18679d926a028c4/data' - : 'community.wave.seqera.io/library/numpy_pandas_python:43a80707feb1fac3' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f727259d394cff047a26f3e3fa3a43e1a7a1c9dc51a35e6def7aa90a2085bb7b/data' + : 'community.wave.seqera.io/library/numpy_pandas_python:cfb38dbf0574e16d'}" input: val sample // run-level name, for the heading diff --git a/modules/local/visualization/error_correction_report/meta.yml b/modules/local/visualization/error_correction_report/meta.yml index 3f9c54b..4588cfa 100644 --- a/modules/local/visualization/error_correction_report/meta.yml +++ b/modules/local/visualization/error_correction_report/meta.yml @@ -54,3 +54,27 @@ authors: - "@BenjaminWehnert1008" maintainers: - "@BenjaminWehnert1008" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/numpy_pandas_python:cfb38dbf0574e16d + build_id: bd-cfb38dbf0574e16d_1 + scan_id: sc-fae0cdb4b6c51968_1 + linux/arm64: + name: community.wave.seqera.io/library/numpy_pandas_python:a15c6f547e2083b8 + build_id: bd-a15c6f547e2083b8_1 + scan_id: sc-931239170a8e2353_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/numpy_pandas_python:7f16bcac97973062 + build_id: bd-7f16bcac97973062_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f727259d394cff047a26f3e3fa3a43e1a7a1c9dc51a35e6def7aa90a2085bb7b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/numpy_pandas_python:648dc1860698d21b + build_id: bd-648dc1860698d21b_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/22/229745e9be125462f1850ac75f13afb0738d30241558908657bfc802c2c6681f/data + conda: + linux/amd64: + lock_file: modules/local/visualization/error_correction_report/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt + linux/arm64: + lock_file: modules/local/visualization/error_correction_report/.conda-lock/linux_arm64-bd-a15c6f547e2083b8_1.txt diff --git a/modules/local/visualization/global_pos_biases_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/visualization/global_pos_biases_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/visualization/global_pos_biases_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(meta), path(variantCounts_filtered_by_library) diff --git a/modules/local/visualization/global_pos_biases_counts/meta.yml b/modules/local/visualization/global_pos_biases_counts/meta.yml index 56ffd1f..b7a2a08 100644 --- a/modules/local/visualization/global_pos_biases_counts/meta.yml +++ b/modules/local/visualization/global_pos_biases_counts/meta.yml @@ -7,8 +7,7 @@ keywords: - rolling mean - sliding window - bias -tools: - +tools: null input: - - meta: type: map @@ -52,3 +51,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + conda: + linux/amd64: + lock_file: modules/local/visualization/global_pos_biases_counts/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/visualization/global_pos_biases_counts/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/visualization/global_pos_biases_cov/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/visualization/global_pos_biases_cov/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/visualization/global_pos_biases_cov/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(meta), path(variantCounts_filtered_by_library) diff --git a/modules/local/visualization/global_pos_biases_cov/meta.yml b/modules/local/visualization/global_pos_biases_cov/meta.yml index 4c71e12..782c488 100644 --- a/modules/local/visualization/global_pos_biases_cov/meta.yml +++ b/modules/local/visualization/global_pos_biases_cov/meta.yml @@ -7,8 +7,7 @@ keywords: - coverage - rolling window - bias -tools: - +tools: null input: - - meta: type: map @@ -47,3 +46,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + conda: + linux/amd64: + lock_file: modules/local/visualization/global_pos_biases_cov/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/visualization/global_pos_biases_cov/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/visualization/logdiff/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/visualization/logdiff/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/visualization/logdiff/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(meta), path(library_completed_variantCounts) diff --git a/modules/local/visualization/logdiff/meta.yml b/modules/local/visualization/logdiff/meta.yml index aae2d92..98ed780 100644 --- a/modules/local/visualization/logdiff/meta.yml +++ b/modules/local/visualization/logdiff/meta.yml @@ -6,8 +6,7 @@ keywords: - visualization - diagnostics - logdiff -tools: - +tools: null input: - - meta: type: map @@ -45,3 +44,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + conda: + linux/amd64: + lock_file: modules/local/visualization/logdiff/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/visualization/logdiff/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/visualization/seqdepth/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt b/modules/local/visualization/seqdepth/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt new file mode 100644 index 0000000..be8d7e8 --- /dev/null +++ b/modules/local/visualization/seqdepth/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt @@ -0,0 +1,2942 @@ +version: 6 +environments: + default: + channels: + - 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libzlib >=1.3.2,<2.0a0 + license: BSD-3-Clause + license_family: BSD + size: 615477 + timestamp: 1786599613561 diff --git a/modules/local/visualization/seqdepth/main.nf b/modules/local/visualization/seqdepth/main.nf index 5b03749..ce18752 100644 --- a/modules/local/visualization/seqdepth/main.nf +++ b/modules/local/visualization/seqdepth/main.nf @@ -5,9 +5,9 @@ process VISUALIZATION_SEQDEPTH { conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/7815f74d3680b875aa8c7be8f78dc77921ec970b99b45a539c5d2225749c0b90/data' - : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:a65d6fd383d85714' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data' + : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7'}" input: tuple val(meta), path(variantCounts_filtered_by_library) diff --git a/modules/local/visualization/seqdepth/meta.yml b/modules/local/visualization/seqdepth/meta.yml index a1f2561..b331288 100644 --- a/modules/local/visualization/seqdepth/meta.yml +++ b/modules/local/visualization/seqdepth/meta.yml @@ -6,8 +6,7 @@ keywords: - visualization - sequencing depth - saturation -tools: - +tools: null input: - - meta: type: map @@ -51,3 +50,27 @@ output: authors: - "@BenjaminWehnert1008" - "@MaximilianStammnitz" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:32f1af0a83a018e7 + build_id: bd-32f1af0a83a018e7_1 + scan_id: sc-337510c2c910aa1c_1 + linux/arm64: + name: community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:880bbdecb19543bb + build_id: bd-880bbdecb19543bb_1 + scan_id: sc-09c9d098a09068b9_1 + singularity: + linux/arm64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:db46247d9810b3e7 + build_id: bd-db46247d9810b3e7_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/02/02db891e505b0ec37ba6de21f08d576b15a95991026542455b209e20959e50b1/data + linux/amd64: + name: oras://community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-dplyr_r-ggplot2_pruned:7202e5d19667bddb + build_id: bd-7202e5d19667bddb_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/79/7988a2e369e98cec897d48bab3e55daddd8a973d9b7491ad27b6b15d550a4c5b/data + conda: + linux/amd64: + lock_file: modules/local/visualization/seqdepth/.conda-lock/linux_amd64-bd-32f1af0a83a018e7_1.txt + linux/arm64: + lock_file: modules/local/visualization/seqdepth/.conda-lock/linux_arm64-bd-880bbdecb19543bb_1.txt diff --git a/modules/local/visualization/summary_report/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt b/modules/local/visualization/summary_report/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt new file mode 100644 index 0000000..e3629c8 --- /dev/null +++ b/modules/local/visualization/summary_report/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt @@ -0,0 +1,556 @@ +version: 6 +environments: + default: + channels: + - 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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/97/977734114fdf9ecc0fbe96d3b2f09901eb1c4490de64d863a18679d926a028c4/data' - : 'community.wave.seqera.io/library/numpy_pandas_python:43a80707feb1fac3' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f727259d394cff047a26f3e3fa3a43e1a7a1c9dc51a35e6def7aa90a2085bb7b/data' + : 'community.wave.seqera.io/library/numpy_pandas_python:cfb38dbf0574e16d'}" input: tuple val(meta), val(run_b64) // base64(JSON) run metadata (params, samples, versions) diff --git a/modules/local/visualization/summary_report/meta.yml b/modules/local/visualization/summary_report/meta.yml index c4c0eb2..239a936 100644 --- a/modules/local/visualization/summary_report/meta.yml +++ b/modules/local/visualization/summary_report/meta.yml @@ -62,3 +62,27 @@ authors: - "@BenjaminWehnert1008" maintainers: - "@BenjaminWehnert1008" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/numpy_pandas_python:cfb38dbf0574e16d + build_id: bd-cfb38dbf0574e16d_1 + scan_id: sc-fae0cdb4b6c51968_1 + linux/arm64: + name: community.wave.seqera.io/library/numpy_pandas_python:a15c6f547e2083b8 + build_id: bd-a15c6f547e2083b8_1 + scan_id: sc-931239170a8e2353_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/numpy_pandas_python:7f16bcac97973062 + build_id: bd-7f16bcac97973062_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f727259d394cff047a26f3e3fa3a43e1a7a1c9dc51a35e6def7aa90a2085bb7b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/numpy_pandas_python:648dc1860698d21b + build_id: bd-648dc1860698d21b_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/22/229745e9be125462f1850ac75f13afb0738d30241558908657bfc802c2c6681f/data + conda: + linux/amd64: + lock_file: modules/local/visualization/summary_report/.conda-lock/linux_amd64-bd-cfb38dbf0574e16d_1.txt + linux/arm64: + lock_file: modules/local/visualization/summary_report/.conda-lock/linux_arm64-bd-a15c6f547e2083b8_1.txt diff --git a/nextflow.config b/nextflow.config index 89bbea4..0697a58 100644 --- a/nextflow.config +++ b/nextflow.config @@ -304,6 +304,7 @@ manifest { nextflowVersion = '!>=25.10.4' version = '1.0.0' doi = '' + diagram = 'docs/images/pipeline.png' } // Nextflow plugins