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Merge pull request #1606 from Genomic-Medicine-Linkoping/add_compression_to_bam2fq

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update samtools/bam2fq: add compression for output fastq file
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Lauri Mesilaakso 2022-05-05 09:37:36 +03:00 committed by GitHub
commit 6bb9be38c5
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GPG key ID: 4AEE18F83AFDEB23
2 changed files with 7 additions and 4 deletions
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2
modules/samtools/bam2fq/main.nf
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@ -45,7 +45,7 @@ process SAMTOOLS_BAM2FQ {
bam2fq \\ bam2fq \\
$args \\ $args \\
-@ $task.cpus \\ -@ $task.cpus \\
$inputbam >${prefix}_interleaved.fq.gz $inputbam | gzip --no-name > ${prefix}_interleaved.fq.gz
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

9
tests/modules/samtools/bam2fq/test.yml
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@ -1,14 +1,15 @@
- name: samtools bam2fq test_samtools_bam2fq_nosplit - name: samtools bam2fq test_samtools_bam2fq_nosplit
command: nextflow run ./tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_nosplit -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bam2fq/nextflow.config command: nextflow run tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_nosplit -c tests/config/nextflow.config
tags: tags:
- samtools/bam2fq - samtools/bam2fq
- samtools - samtools
files: files:
- path: output/samtools/test_interleaved.fq.gz - path: output/samtools/test_interleaved.fq.gz
md5sum: d733e66d29a4b366bf9df8c42f845256 - path: output/samtools/versions.yml
md5sum: 4973eac1b6a8f090d5fcd4456d65a894
- name: samtools bam2fq test_samtools_bam2fq_withsplit - name: samtools bam2fq test_samtools_bam2fq_withsplit
command: nextflow run ./tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_withsplit -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bam2fq/nextflow.config command: nextflow run tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_withsplit -c tests/config/nextflow.config
tags: tags:
- samtools/bam2fq - samtools/bam2fq
- samtools - samtools
@ -21,3 +22,5 @@
md5sum: 709872fc2910431b1e8b7074bfe38c67 md5sum: 709872fc2910431b1e8b7074bfe38c67
- path: output/samtools/test_singleton.fq.gz - path: output/samtools/test_singleton.fq.gz
md5sum: 709872fc2910431b1e8b7074bfe38c67 md5sum: 709872fc2910431b1e8b7074bfe38c67
- path: output/samtools/versions.yml
md5sum: e92d21bbcda2fed7cb438d95c51edff0