From 50dff9bc3830a50cc34933ee1cb9160fe87844dd Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Sun, 11 Feb 2024 23:09:06 -0600 Subject: [PATCH 1/8] test(narfmap): Add segfault test --- .../narfmap/align/tests/segfault.nf.test | 54 +++++++++++++++++++ .../narfmap/align/tests/segfault.nf.test.snap | 21 ++++++++ tests/config/nf-test.config | 2 +- 3 files changed, 76 insertions(+), 1 deletion(-) create mode 100644 modules/nf-core/narfmap/align/tests/segfault.nf.test create mode 100644 modules/nf-core/narfmap/align/tests/segfault.nf.test.snap diff --git a/modules/nf-core/narfmap/align/tests/segfault.nf.test b/modules/nf-core/narfmap/align/tests/segfault.nf.test new file mode 100644 index 00000000000..9b5252355a8 --- /dev/null +++ b/modules/nf-core/narfmap/align/tests/segfault.nf.test @@ -0,0 +1,54 @@ +nextflow_process { + + name "Test Process NARFMAP_ALIGN" + script "../main.nf" + process "NARFMAP_ALIGN" + tag "modules" + tag "modules_nfcore" + tag "narfmap" + tag "narfmap/align" + tag "bug" + + test("This should segfault") { + + setup { + run("NARFMAP_HASHTABLE") { + script "../../hashtable/main.nf" + process { + """ + input[0] = [ + [id:'test'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/GRCh38_chr21.fa', checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file('https://raw.githubusercontent.com/nf-core/test-datasets/nascent/testdata/SRX882903_T2.fastq.gz', checkIfExists: true) + ] + input[1] = NARFMAP_HASHTABLE.out.hashmap + input[2] = false //sort + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.bam[0][1]).name, + file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, + file(process.out.versions[0]).name + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/narfmap/align/tests/segfault.nf.test.snap b/modules/nf-core/narfmap/align/tests/segfault.nf.test.snap new file mode 100644 index 00000000000..8c5d27bec15 --- /dev/null +++ b/modules/nf-core/narfmap/align/tests/segfault.nf.test.snap @@ -0,0 +1,21 @@ +{ + "This should segfault": { + "content": [ + "test.bam", + [ + "decompHashTableCtxInit...", + "decompHashTableHeader...", + "decompHashTableLiterals...", + "decompHashTableExtIndex...", + "decompHashTableAutoHits...", + "decompHashTableSetFlags..." + ], + "versions.yml" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-11T23:08:34.922392857" + } +} \ No newline at end of file diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config index 269f2dc3ca1..2c4467c3acb 100644 --- a/tests/config/nf-test.config +++ b/tests/config/nf-test.config @@ -7,7 +7,7 @@ params { process { cpus = 2 - memory = 3.GB + memory = 6.GB time = 2.h } From 574f95b041af95b90166d0e580f204f8d16be73f Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Sun, 11 Feb 2024 23:09:21 -0600 Subject: [PATCH 2/8] fix(narfmap): Clean up log error --- modules/nf-core/narfmap/align/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/narfmap/align/main.nf b/modules/nf-core/narfmap/align/main.nf index 01c7b57595d..72a722c5226 100644 --- a/modules/nf-core/narfmap/align/main.nf +++ b/modules/nf-core/narfmap/align/main.nf @@ -34,7 +34,7 @@ process NARFMAP_ALIGN { $args \\ --num-threads $task.cpus \\ $reads_command \\ - 2> ${prefix}.narfmap.log \\ + 2> >(tee ${prefix}.narfmap.log >&2) \\ | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam - cat <<-END_VERSIONS > versions.yml From 79e4bcb200965a309d19983237348e95eb7a24f0 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 12 Feb 2024 13:58:17 -0600 Subject: [PATCH 3/8] test(narfmap): Should segfault --- modules/nf-core/narfmap/align/tests/segfault.nf.test | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/narfmap/align/tests/segfault.nf.test b/modules/nf-core/narfmap/align/tests/segfault.nf.test index 9b5252355a8..f90f329cff1 100644 --- a/modules/nf-core/narfmap/align/tests/segfault.nf.test +++ b/modules/nf-core/narfmap/align/tests/segfault.nf.test @@ -40,7 +40,9 @@ nextflow_process { then { assertAll ( - { assert process.success }, + // FIXME this should fail until this issue is fixed + // https://github.com/edmundmiller/NARFMAP/issues/10 + { assert process.failed }, { assert snapshot( file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, From 1d4c0e03fd6d1c241cb2c1def070beb2a5e3ba5b Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 8 Jul 2024 09:41:06 -0500 Subject: [PATCH 4/8] chore(narfmap): Bump to 1.4.2 --- modules/nf-core/narfmap/align/environment.yml | 2 +- modules/nf-core/narfmap/align/main.nf | 4 ++-- modules/nf-core/narfmap/hashtable/environment.yml | 2 +- modules/nf-core/narfmap/hashtable/main.nf | 6 ++---- 4 files changed, 6 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/narfmap/align/environment.yml b/modules/nf-core/narfmap/align/environment.yml index 39b099a4630..62629829d36 100644 --- a/modules/nf-core/narfmap/align/environment.yml +++ b/modules/nf-core/narfmap/align/environment.yml @@ -5,7 +5,7 @@ channels: - defaults dependencies: # renovate: datasource=conda depName=bioconda/narfmap - - narfmap=1.4.0 + - narfmap=1.4.2 # renovate: datasource=conda depName=bioconda/samtools - samtools=1.18 - pigz=2.8 diff --git a/modules/nf-core/narfmap/align/main.nf b/modules/nf-core/narfmap/align/main.nf index 72a722c5226..3b91375a200 100644 --- a/modules/nf-core/narfmap/align/main.nf +++ b/modules/nf-core/narfmap/align/main.nf @@ -5,8 +5,8 @@ process NARFMAP_ALIGN { // TODO Add a singularity image conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'nf-core/modules/narfmap_align:narfmap--8a04bcf8bd9b6242': - 'nf-core/modules/narfmap_align:narfmap--8a04bcf8bd9b6242' }" + 'oras://community.wave.seqera.io/library/narfmap_align:8bad41386eab9997': + 'community.wave.seqera.io/library/narfmap_align:517a1fed8e4e84c1' }" input: tuple val(meta) , path(reads) diff --git a/modules/nf-core/narfmap/hashtable/environment.yml b/modules/nf-core/narfmap/hashtable/environment.yml index 84a8240cc6b..d4492db958e 100644 --- a/modules/nf-core/narfmap/hashtable/environment.yml +++ b/modules/nf-core/narfmap/hashtable/environment.yml @@ -5,4 +5,4 @@ channels: - defaults dependencies: # renovate: datasource=conda depName=bioconda/narfmap - - bioconda::narfmap=1.4.0 + - bioconda::narfmap=1.4.2 diff --git a/modules/nf-core/narfmap/hashtable/main.nf b/modules/nf-core/narfmap/hashtable/main.nf index 307846ec59c..df065c12583 100644 --- a/modules/nf-core/narfmap/hashtable/main.nf +++ b/modules/nf-core/narfmap/hashtable/main.nf @@ -2,12 +2,10 @@ process NARFMAP_HASHTABLE { tag "$fasta" label 'process_high' - // TODO Add a singularity image - // TODO Make a seperate image conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'nf-core/modules/narfmap_align:narfmap--8a04bcf8bd9b6242': - 'nf-core/modules/narfmap_align:narfmap--8a04bcf8bd9b6242' }" + 'https://depot.galaxyproject.org/singularity/narfmap:1.4.2--h43eeafb_0': + 'biocontainers/narfmap:1.4.2--h43eeafb_0' }" input: tuple val(meta), path(fasta) From b7a6475bac6b77db34b43f03d6e3325a33978b3d Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 8 Jul 2024 10:19:20 -0500 Subject: [PATCH 5/8] test(narfmap): Mark test as passing https://github.com/edmundmiller/NARFMAP/issues/10 --- modules/nf-core/narfmap/align/tests/segfault.nf.test | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/modules/nf-core/narfmap/align/tests/segfault.nf.test b/modules/nf-core/narfmap/align/tests/segfault.nf.test index f90f329cff1..9b5252355a8 100644 --- a/modules/nf-core/narfmap/align/tests/segfault.nf.test +++ b/modules/nf-core/narfmap/align/tests/segfault.nf.test @@ -40,9 +40,7 @@ nextflow_process { then { assertAll ( - // FIXME this should fail until this issue is fixed - // https://github.com/edmundmiller/NARFMAP/issues/10 - { assert process.failed }, + { assert process.success }, { assert snapshot( file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, From ab2efb71923e2c3215978c20b9efd93a48c8f82a Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 8 Jul 2024 10:39:31 -0500 Subject: [PATCH 6/8] style: Add extra tag for nf-core/lint --- modules/nf-core/narfmap/align/tests/main.nf.test | 1 + modules/nf-core/narfmap/align/tests/segfault.nf.test | 1 + 2 files changed, 2 insertions(+) diff --git a/modules/nf-core/narfmap/align/tests/main.nf.test b/modules/nf-core/narfmap/align/tests/main.nf.test index 9286a88439b..c645672c476 100644 --- a/modules/nf-core/narfmap/align/tests/main.nf.test +++ b/modules/nf-core/narfmap/align/tests/main.nf.test @@ -7,6 +7,7 @@ nextflow_process { tag "modules_nfcore" tag "narfmap" tag "narfmap/align" + tag "narfmap/hashtable" test("sarscov2 - fastq, hashtable, false") { diff --git a/modules/nf-core/narfmap/align/tests/segfault.nf.test b/modules/nf-core/narfmap/align/tests/segfault.nf.test index 9b5252355a8..0baf5f75967 100644 --- a/modules/nf-core/narfmap/align/tests/segfault.nf.test +++ b/modules/nf-core/narfmap/align/tests/segfault.nf.test @@ -7,6 +7,7 @@ nextflow_process { tag "modules_nfcore" tag "narfmap" tag "narfmap/align" + tag "narfmap/hashtable" tag "bug" test("This should segfault") { From f1d713f44ef09fc1d69136230a9d7389a5c9cdf1 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 8 Jul 2024 11:31:20 -0500 Subject: [PATCH 7/8] test: Update all the snapshot declarations --- .../nf-core/narfmap/align/tests/main.nf.test | 38 ++++-- .../narfmap/align/tests/main.nf.test.snap | 128 +++++++++++++++--- .../narfmap/align/tests/segfault.nf.test | 6 +- .../narfmap/align/tests/segfault.nf.test.snap | 19 ++- .../narfmap/hashtable/tests/main.nf.test.snap | 8 ++ 5 files changed, 162 insertions(+), 37 deletions(-) diff --git a/modules/nf-core/narfmap/align/tests/main.nf.test b/modules/nf-core/narfmap/align/tests/main.nf.test index c645672c476..10b3f4d0e29 100644 --- a/modules/nf-core/narfmap/align/tests/main.nf.test +++ b/modules/nf-core/narfmap/align/tests/main.nf.test @@ -42,10 +42,12 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( + process.out.bam, + process.out.versions, file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, - file(process.out.versions[0]).name - ).match() } + ).match() + } ) } @@ -84,10 +86,12 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( + process.out.bam, + process.out.versions, file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, - file(process.out.versions[0]).name - ).match() } + ).match() + } ) } @@ -129,10 +133,12 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( + process.out.bam, + process.out.versions, file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, - file(process.out.versions[0]).name - ).match() } + ).match() + } ) } @@ -174,10 +180,12 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( + process.out.bam, + process.out.versions, file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, - file(process.out.versions[0]).name - ).match() } + ).match() + } ) } @@ -219,10 +227,12 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( + process.out.bam, + process.out.versions, file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, - file(process.out.versions[0]).name - ).match() } + ).match() + } ) } @@ -265,10 +275,12 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( + process.out.bam, + process.out.versions, file(process.out.bam[0][1]).name, - file(process.out.log[0][1]).name, - file(process.out.versions[0]).name - ).match() } + file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, + ).match() + } ) } diff --git a/modules/nf-core/narfmap/align/tests/main.nf.test.snap b/modules/nf-core/narfmap/align/tests/main.nf.test.snap index 32d88a27965..09013b98931 100644 --- a/modules/nf-core/narfmap/align/tests/main.nf.test.snap +++ b/modules/nf-core/narfmap/align/tests/main.nf.test.snap @@ -1,6 +1,18 @@ { "homo_sapiens - [fastq1, fastq2], hashtable, true": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,5c407c8e621fc931af17a585526598bf" + ] + ], + [ + "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" + ], "test.bam", [ "decompHashTableCtxInit...", @@ -9,21 +21,53 @@ "decompHashTableExtIndex...", "decompHashTableAutoHits...", "decompHashTableSetFlags..." - ], - "versions.yml" + ] ], - "timestamp": "2023-11-23T10:12:03.844836279" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-08T11:45:10.095839411" }, "sarscov2 - [fastq1, fastq2], hashtable, true - stub": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" + ], "test.bam", - "test.log", - "versions.yml" + [ + + ] ], - "timestamp": "2023-11-22T13:41:18.016853266" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-08T11:45:22.364107512" }, "sarscov2 - fastq, hashtable, false": { "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,ea3a6f419b6c8f91e99603058c608124" + ] + ], + [ + "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" + ], "test.bam", [ "decompHashTableCtxInit...", @@ -32,13 +76,28 @@ "decompHashTableExtIndex...", "decompHashTableAutoHits...", "decompHashTableSetFlags..." - ], - "versions.yml" + ] ], - "timestamp": "2023-11-23T10:11:33.956661024" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-08T11:43:57.96792573" }, "sarscov2 - fastq, hashtable, true": { "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,e2632fce5442e05210edd516715489c4" + ] + ], + [ + "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" + ], "test.bam", [ "decompHashTableCtxInit...", @@ -47,13 +106,28 @@ "decompHashTableExtIndex...", "decompHashTableAutoHits...", "decompHashTableSetFlags..." - ], - "versions.yml" + ] ], - "timestamp": "2023-11-23T10:11:40.270598375" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-08T11:44:17.486586239" }, "sarscov2 - [fastq1, fastq2], hashtable, false": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,ef0c12ae27778b906fd4f822ef7ce074" + ] + ], + [ + "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" + ], "test.bam", [ "decompHashTableCtxInit...", @@ -62,13 +136,28 @@ "decompHashTableExtIndex...", "decompHashTableAutoHits...", "decompHashTableSetFlags..." - ], - "versions.yml" + ] ], - "timestamp": "2023-11-23T10:11:46.928978876" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-08T11:44:48.178604348" }, "sarscov2 - [fastq1, fastq2], hashtable, true": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,54965e6a11a9c31b1ae3c7e896c96c32" + ] + ], + [ + "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" + ], "test.bam", [ "decompHashTableCtxInit...", @@ -77,9 +166,12 @@ "decompHashTableExtIndex...", "decompHashTableAutoHits...", "decompHashTableSetFlags..." - ], - "versions.yml" + ] ], - "timestamp": "2023-11-23T10:11:53.506727278" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-08T11:44:55.858525101" } } \ No newline at end of file diff --git a/modules/nf-core/narfmap/align/tests/segfault.nf.test b/modules/nf-core/narfmap/align/tests/segfault.nf.test index 0baf5f75967..88a42a03330 100644 --- a/modules/nf-core/narfmap/align/tests/segfault.nf.test +++ b/modules/nf-core/narfmap/align/tests/segfault.nf.test @@ -43,10 +43,12 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( + process.out.bam, + process.out.versions, file(process.out.bam[0][1]).name, file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") }, - file(process.out.versions[0]).name - ).match() } + ).match() + } ) } diff --git a/modules/nf-core/narfmap/align/tests/segfault.nf.test.snap b/modules/nf-core/narfmap/align/tests/segfault.nf.test.snap index 8c5d27bec15..9708b4ec130 100644 --- a/modules/nf-core/narfmap/align/tests/segfault.nf.test.snap +++ b/modules/nf-core/narfmap/align/tests/segfault.nf.test.snap @@ -1,6 +1,18 @@ { "This should segfault": { "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,c38463b4da3a56010093cf2ce7634b86" + ] + ], + [ + "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7" + ], "test.bam", [ "decompHashTableCtxInit...", @@ -9,13 +21,12 @@ "decompHashTableExtIndex...", "decompHashTableAutoHits...", "decompHashTableSetFlags..." - ], - "versions.yml" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-11T23:08:34.922392857" + "timestamp": "2024-07-08T11:46:14.084669293" } } \ No newline at end of file diff --git a/modules/nf-core/narfmap/hashtable/tests/main.nf.test.snap b/modules/nf-core/narfmap/hashtable/tests/main.nf.test.snap index d1676be9917..2f5b5edaf95 100644 --- a/modules/nf-core/narfmap/hashtable/tests/main.nf.test.snap +++ b/modules/nf-core/narfmap/hashtable/tests/main.nf.test.snap @@ -4,6 +4,10 @@ "narfmap", "versions.yml" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2023-12-15T17:42:36.677592114" }, "sarscov2 - fasta": { @@ -11,6 +15,10 @@ "narfmap", "versions.yml" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2023-12-15T17:42:32.074476297" } } \ No newline at end of file From fc03ab91daf5b3c30cfa1f24e6e7699375f026e8 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 8 Jul 2024 11:55:26 -0500 Subject: [PATCH 8/8] chore: Add a TODO for poddar's test --- modules/nf-core/narfmap/align/tests/segfault.nf.test | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/modules/nf-core/narfmap/align/tests/segfault.nf.test b/modules/nf-core/narfmap/align/tests/segfault.nf.test index 88a42a03330..3e89e97f37d 100644 --- a/modules/nf-core/narfmap/align/tests/segfault.nf.test +++ b/modules/nf-core/narfmap/align/tests/segfault.nf.test @@ -54,4 +54,14 @@ nextflow_process { } + // TODO + // https://nfcore.slack.com/archives/CGFUX04HZ/p1718268624579699?thread_ts=1718108323.285709&cid=CGFUX04HZ + // https://ftp.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_HiSeq_HG002_Homogeneity-10953946/HG002_HiSeq300x_fastq/140528_D00360_0018_AH8VC6ADXX/Project_RM8391_RM8392/Sample_2A1/2A1_CGATGT_L001_R1_001.fastq.gz + // https://ftp.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_HiSeq_HG002_Homogeneity-10953946/HG002_HiSeq300x_fastq/140528_D00360_0018_AH8VC6ADXX/Project_RM8391_RM8392/Sample_2A1/2A1_CGATGT_L001_R2_001.fastq.gz + // {{dragen}} \ + // -r /home/tigem/h.poddar/short_reads_pipelines/ref_genome/GRCh37/hash/ \ + // -1 /home/tigem/h.poddar/DRAGMAP/2A1_CGATGT_L001_R1_001.fastq.gz \ + // -2 /home/tigem/h.poddar/DRAGMAP/2A1_CGATGT_L001_R2_001.fastq.gz \ + // | samtools view -h -O BAM - > aligned.bam + }