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Resolve the BWA index prefix without find(1) - #95
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BenjaminWehnert1008 wants to merge 1 commit into
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MERGE_ALIGN failed with exit 127 and ".command.sh: line 2: find: command not found" on both real-data shards of -profile singularity, the first time that leg has ever run (conda and singularity are excluded from the matrix unless a PR targets master, so #54 is the first PR to exercise them). Seqera Containers builds the two variants of the same conda spec on different userlands: the Docker image of bwa_samtools_vsearch is Ubuntu 24.04 based and carries /usr/bin/find, while the Singularity image is built from mambaorg/micromamba:2-amazon2023, whose base ships no findutils. Wave's own build script already patches around the same gap for `which`. Of everything this module calls, only find is affected - sed, awk, cat, mv and head are all present in that base, which is also why BWA_INDEX (mkdir) succeeded. Globbing with bash parameter expansion needs no external binary, and this was the only find(1) call site in the repository. The leading ./ is kept deliberately: find printed ./bwa/<prefix>.amb, so $INDEX was ./bwa/<prefix>, and bwa records that string in the BAM's @pg header. Dropping it would change every sorted BAM's md5 and move the nf-test snapshot for no reason. Verified against the old command: both yield ./bwa/GID1A. An empty index directory now fails with a clear message instead of passing a literal glob to bwa mem.
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MERGE_ALIGN failed with exit 127 and ".command.sh: line 2: find: command not found" on both real-data shards of -profile singularity, the first time that leg has ever run (conda and singularity are excluded from the matrix unless a PR targets master, so #54 is the first PR to exercise them).
Seqera Containers builds the two variants of the same conda spec on different userlands: the Docker image of bwa_samtools_vsearch is Ubuntu 24.04 based and carries /usr/bin/find, while the Singularity image is built from mambaorg/micromamba:2-amazon2023, whose base ships no findutils. Wave's own build script already patches around the same gap for
which. Of everything this module calls, only find is affected - sed, awk, cat, mv and head are all present in that base, which is also why BWA_INDEX (mkdir) succeeded.Globbing with bash parameter expansion needs no external binary, and this was the only find(1) call site in the repository. The leading ./ is kept deliberately: find printed ./bwa/.amb, so $INDEX was ./bwa/, and bwa records that string in the BAM's @pg header. Dropping it would change every sorted BAM's md5 and move the nf-test snapshot for no reason. Verified against the old command: both yield ./bwa/GID1A. An empty index directory now fails with a clear message instead of passing a literal glob to bwa mem.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).