This commit reverts most of f264f49639e7d4d9e8b2e9021b71b8df056c49f2.
It turns out that the input file needs to be filtered with -F0x400, so even if the user provides a BAM file we need samtools view
PR checklist
[ ] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).
This commit reverts most of f264f49639e7d4d9e8b2e9021b71b8df056c49f2. It turns out that the input file needs to be filtered with
-F0x400
, so even if the user provides a BAM file we needsamtools view
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).