From 1654c4dcd1a402b2e03786390f1a125243e1eade Mon Sep 17 00:00:00 2001 From: Helle Rus Povlsen Date: Thu, 15 Aug 2024 16:14:35 +0200 Subject: [PATCH 1/5] update output dir for bamtofastq10x --- modules/nf-core/bamtofastq10x/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/bamtofastq10x/main.nf b/modules/nf-core/bamtofastq10x/main.nf index be1b14415be..f5ae6e0e4c1 100644 --- a/modules/nf-core/bamtofastq10x/main.nf +++ b/modules/nf-core/bamtofastq10x/main.nf @@ -11,8 +11,8 @@ process BAMTOFASTQ10X { tuple val(meta), path(bam) output: - tuple val(meta), path("*.fastq.gz"), emit: fastq - path "versions.yml" , emit: versions + tuple val(meta), path("${meta.id}/**/*.fastq.gz"), emit: fastq + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -24,7 +24,7 @@ process BAMTOFASTQ10X { bamtofastq \\ $args \\ $bam \\ - ${prefix}.fastq.gz + $prefix cat <<-END_VERSIONS > versions.yml "${task.process}": From 7379f2ac0ec7e8f00df9acac4dd566245535223e Mon Sep 17 00:00:00 2001 From: Helle Rus Povlsen Date: Fri, 13 Sep 2024 12:58:58 +0200 Subject: [PATCH 2/5] update path for output fastq --- modules/nf-core/bamtofastq10x/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/bamtofastq10x/main.nf b/modules/nf-core/bamtofastq10x/main.nf index f5ae6e0e4c1..8cd52bca0df 100644 --- a/modules/nf-core/bamtofastq10x/main.nf +++ b/modules/nf-core/bamtofastq10x/main.nf @@ -11,8 +11,8 @@ process BAMTOFASTQ10X { tuple val(meta), path(bam) output: - tuple val(meta), path("${meta.id}/**/*.fastq.gz"), emit: fastq - path "versions.yml" , emit: versions + tuple val(meta), path("**/*.fastq.gz"), emit: fastq + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when From 38eebd0bba206e3d16ce8bb7aea06dfc163ffae3 Mon Sep 17 00:00:00 2001 From: Helle Rus Povlsen Date: Fri, 27 Sep 2024 12:21:15 +0200 Subject: [PATCH 3/5] update snapshot --- .../bamtofastq10x/tests/main.nf.test.snap | 22 ++++++++----------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap b/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap index d534674592d..39f81abfe0d 100644 --- a/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap +++ b/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap @@ -8,11 +8,9 @@ "id": "test" }, [ - [ - "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0", - "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f", - "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002" - ] + "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0", + "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f", + "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002" ] ] ], @@ -25,11 +23,9 @@ "id": "test" }, [ - [ - "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0", - "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f", - "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002" - ] + "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0", + "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f", + "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002" ] ] ], @@ -39,9 +35,9 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-22T16:43:24.999397" + "timestamp": "2024-09-13T13:31:25.289414" } } \ No newline at end of file From 2164bddf8ec7a308ff691bf4e566b796384616af Mon Sep 17 00:00:00 2001 From: Helle Rus Povlsen Date: Wed, 2 Oct 2024 12:50:13 +0200 Subject: [PATCH 4/5] update stub --- modules/nf-core/bamtofastq10x/main.nf | 3 ++- modules/nf-core/bamtofastq10x/tests/main.nf.test.snap | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/bamtofastq10x/main.nf b/modules/nf-core/bamtofastq10x/main.nf index 8cd52bca0df..bff379c19ee 100644 --- a/modules/nf-core/bamtofastq10x/main.nf +++ b/modules/nf-core/bamtofastq10x/main.nf @@ -35,7 +35,8 @@ process BAMTOFASTQ10X { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.fastq.gz + mkdir -p ${prefix}/bamtofastq10x + touch ${prefix}/bamtofastq10x/bamtofastq.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap b/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap index 39f81abfe0d..7f1330a5c7a 100644 --- a/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap +++ b/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap @@ -38,6 +38,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T13:31:25.289414" + "timestamp": "2024-10-02T12:31:07.674368" } } \ No newline at end of file From 5084659b44ed99b19e8f89e47d357f707facded3 Mon Sep 17 00:00:00 2001 From: Helle Rus Povlsen Date: Wed, 2 Oct 2024 13:19:09 +0200 Subject: [PATCH 5/5] update output definition in meta.yml --- modules/nf-core/bamtofastq10x/meta.yml | 4 ++-- modules/nf-core/bamtofastq10x/tests/main.nf.test.snap | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/bamtofastq10x/meta.yml b/modules/nf-core/bamtofastq10x/meta.yml index ace49c25182..f3e5dfcaa24 100644 --- a/modules/nf-core/bamtofastq10x/meta.yml +++ b/modules/nf-core/bamtofastq10x/meta.yml @@ -37,10 +37,10 @@ output: description: | Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]` - - "*.fastq.gz": + - "**/*.fastq.gz": type: file description: fastq compressed file - pattern: "*.fastq.gz" + pattern: "**/*.fastq.gz" - versions: - versions.yml: type: file diff --git a/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap b/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap index 7f1330a5c7a..fd531091017 100644 --- a/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap +++ b/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap @@ -38,6 +38,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-02T12:31:07.674368" + "timestamp": "2024-10-02T12:56:21.808042" } } \ No newline at end of file