From 550390345785fe0ebb1835616f895af2bdadf122 Mon Sep 17 00:00:00 2001 From: ljmesi <37740329+ljmesi@users.noreply.github.com> Date: Tue, 3 May 2022 09:46:04 +0200 Subject: [PATCH 1/5] Add compression for output fastq file --- modules/samtools/bam2fq/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/samtools/bam2fq/main.nf b/modules/samtools/bam2fq/main.nf index 5d6aa79d..554af48b 100644 --- a/modules/samtools/bam2fq/main.nf +++ b/modules/samtools/bam2fq/main.nf @@ -45,7 +45,7 @@ process SAMTOOLS_BAM2FQ { bam2fq \\ $args \\ -@ $task.cpus \\ - $inputbam >${prefix}_interleaved.fq.gz + $inputbam | gzip > ${prefix}_interleaved.fq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": From 59d6e6e1dd0dc5cbfff7d431725caeaf201c40e4 Mon Sep 17 00:00:00 2001 From: ljmesi <37740329+ljmesi@users.noreply.github.com> Date: Tue, 3 May 2022 09:56:50 +0200 Subject: [PATCH 2/5] Add updated md5sums --- tests/modules/samtools/bam2fq/test.yml | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/tests/modules/samtools/bam2fq/test.yml b/tests/modules/samtools/bam2fq/test.yml index 213c7a2d..6fcc9c22 100644 --- a/tests/modules/samtools/bam2fq/test.yml +++ b/tests/modules/samtools/bam2fq/test.yml @@ -1,17 +1,19 @@ - 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: - - samtools/bam2fq - samtools + - samtools/bam2fq files: - path: output/samtools/test_interleaved.fq.gz - md5sum: d733e66d29a4b366bf9df8c42f845256 + md5sum: 7a57a8ab53dd1d799cca67a85c47ccd9 + - path: output/samtools/versions.yml + md5sum: 4973eac1b6a8f090d5fcd4456d65a894 - 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: - - samtools/bam2fq - samtools + - samtools/bam2fq files: - path: output/samtools/test_1.fq.gz md5sum: 1c84aadcdca10e97be2b5b6ce773f5ed @@ -21,3 +23,5 @@ md5sum: 709872fc2910431b1e8b7074bfe38c67 - path: output/samtools/test_singleton.fq.gz md5sum: 709872fc2910431b1e8b7074bfe38c67 + - path: output/samtools/versions.yml + md5sum: e92d21bbcda2fed7cb438d95c51edff0 From 5510ea39fe638594bc26ac34cadf4a84bf27d159 Mon Sep 17 00:00:00 2001 From: ljmesi <37740329+ljmesi@users.noreply.github.com> Date: Tue, 3 May 2022 15:18:09 +0200 Subject: [PATCH 3/5] Test --no-name to solve inconsistent checksums --- modules/samtools/bam2fq/main.nf | 2 +- tests/modules/samtools/bam2fq/test.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/samtools/bam2fq/main.nf b/modules/samtools/bam2fq/main.nf index 554af48b..9301d1d3 100644 --- a/modules/samtools/bam2fq/main.nf +++ b/modules/samtools/bam2fq/main.nf @@ -45,7 +45,7 @@ process SAMTOOLS_BAM2FQ { bam2fq \\ $args \\ -@ $task.cpus \\ - $inputbam | gzip > ${prefix}_interleaved.fq.gz + $inputbam | gzip --no-name > ${prefix}_interleaved.fq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/tests/modules/samtools/bam2fq/test.yml b/tests/modules/samtools/bam2fq/test.yml index 6fcc9c22..674730d7 100644 --- a/tests/modules/samtools/bam2fq/test.yml +++ b/tests/modules/samtools/bam2fq/test.yml @@ -1,8 +1,8 @@ - name: samtools bam2fq test_samtools_bam2fq_nosplit command: nextflow run tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_nosplit -c tests/config/nextflow.config tags: - - samtools - samtools/bam2fq + - samtools files: - path: output/samtools/test_interleaved.fq.gz md5sum: 7a57a8ab53dd1d799cca67a85c47ccd9 @@ -12,8 +12,8 @@ - name: samtools bam2fq test_samtools_bam2fq_withsplit command: nextflow run tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_withsplit -c tests/config/nextflow.config tags: - - samtools - samtools/bam2fq + - samtools files: - path: output/samtools/test_1.fq.gz md5sum: 1c84aadcdca10e97be2b5b6ce773f5ed From a39fa4e003efce395debe34de57c5b28472c762c Mon Sep 17 00:00:00 2001 From: ljmesi <37740329+ljmesi@users.noreply.github.com> Date: Tue, 3 May 2022 15:47:49 +0200 Subject: [PATCH 4/5] Fix checksum for one file --- tests/modules/samtools/bam2fq/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/samtools/bam2fq/test.yml b/tests/modules/samtools/bam2fq/test.yml index 674730d7..9d641e4a 100644 --- a/tests/modules/samtools/bam2fq/test.yml +++ b/tests/modules/samtools/bam2fq/test.yml @@ -5,7 +5,7 @@ - samtools files: - path: output/samtools/test_interleaved.fq.gz - md5sum: 7a57a8ab53dd1d799cca67a85c47ccd9 + md5sum: 7290d2d8dbef0fa57c0e2f28b5db1bf8 - path: output/samtools/versions.yml md5sum: 4973eac1b6a8f090d5fcd4456d65a894 From be8ce6de2ae833802a44b9c2b3991dbb56eb43a4 Mon Sep 17 00:00:00 2001 From: ljmesi <37740329+ljmesi@users.noreply.github.com> Date: Thu, 5 May 2022 08:32:45 +0200 Subject: [PATCH 5/5] Remove variable md5sum from the tests --- tests/modules/samtools/bam2fq/test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/modules/samtools/bam2fq/test.yml b/tests/modules/samtools/bam2fq/test.yml index 9d641e4a..4f9472e5 100644 --- a/tests/modules/samtools/bam2fq/test.yml +++ b/tests/modules/samtools/bam2fq/test.yml @@ -5,7 +5,6 @@ - samtools files: - path: output/samtools/test_interleaved.fq.gz - md5sum: 7290d2d8dbef0fa57c0e2f28b5db1bf8 - path: output/samtools/versions.yml md5sum: 4973eac1b6a8f090d5fcd4456d65a894