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Md cram #735
Md cram #735
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Do we still need the |
Yes for the cases where we don't do duplicate marking. It would be simplified though by importing cram_qc in bam_to_cram |
Good enough for me |
TODO:
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<3
still a couple of tests to fix 😄 |
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Love how it's now simplified
therfore I broke now everything 🙈 |
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
nextflow.config
Outdated
@@ -43,7 +43,7 @@ params { | |||
// Preprocessing | |||
aligner = 'bwa-mem' // Default is bwa-mem, bwa-mem2 and dragmap can be used too | |||
use_gatk_spark = null // GATK Spark implementation of their tools in local mode not used by default | |||
save_bam_mapped = false // Mapped BAMs not saved | |||
save_mapped = false // Mapped BAMs not saved |
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save_mapped = false // Mapped BAMs not saved | |
save_mapped = false // Mapped files not saved |
nextflow.config
Outdated
@@ -43,7 +43,7 @@ params { | |||
// Preprocessing | |||
aligner = 'bwa-mem' // Default is bwa-mem, bwa-mem2 and dragmap can be used too | |||
use_gatk_spark = null // GATK Spark implementation of their tools in local mode not used by default | |||
save_bam_mapped = false // Mapped BAMs not saved | |||
save_mapped = false // Mapped BAMs not saved | |||
save_output_as_bam = false //Output files from preprocessing are saved as bam and not as cram files |
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save_output_as_bam = false //Output files from preprocessing are saved as bam and not as cram files | |
save_output_as_bam = false // Output files from preprocessing are saved as bam and not as cram files |
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).