From c2825b1d041c9c1a0420850c4c6cd59e9b82e680 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Wed, 13 Mar 2024 10:51:03 +0000 Subject: [PATCH 1/5] add paths in output directive --- modules/nf-core/cellranger/count/main.nf | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf index 42aa09c9f5b..92771c6fe6d 100644 --- a/modules/nf-core/cellranger/count/main.nf +++ b/modules/nf-core/cellranger/count/main.nf @@ -9,8 +9,10 @@ process CELLRANGER_COUNT { path reference output: - tuple val(meta), path("**/outs/**"), emit: outs - path "versions.yml" , emit: versions + tuple val(meta), path("**/outs/**") , emit: outs + tuple val(meta), path("**/outs/filtered_feature_bc_matrix**"), emit: filtered + tuple val(meta), path("**/outs/raw_feature_bc_matrix**") , emit: raw + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when From c01cae750398035e26be93c9cb8525910d20ebff Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Wed, 13 Mar 2024 10:54:39 +0000 Subject: [PATCH 2/5] update meta.yml --- modules/nf-core/cellranger/count/meta.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/modules/nf-core/cellranger/count/meta.yml b/modules/nf-core/cellranger/count/meta.yml index 1f1768a857b..562449769b8 100644 --- a/modules/nf-core/cellranger/count/meta.yml +++ b/modules/nf-core/cellranger/count/meta.yml @@ -40,6 +40,14 @@ output: type: file description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list pattern: "${meta.id}/outs/*" + - filtered: + type: file + description: Files containing the filtered outputs of Cell Ranger. + pattern: "**/outs/filtered_feature_bc_matrix**" + - raw: + type: file + description: Files containing the raw outputs of Cell Ranger. + pattern: "**/outs/raw_feature_bc_matrix**" - versions: type: file description: File containing software version From 8023539bc431f085b1940a88f70e4e13fbe77163 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Mon, 18 Mar 2024 11:23:30 +0000 Subject: [PATCH 3/5] add stub file generation --- modules/nf-core/cellranger/count/main.nf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf index 92771c6fe6d..eeea8ccc203 100644 --- a/modules/nf-core/cellranger/count/main.nf +++ b/modules/nf-core/cellranger/count/main.nf @@ -34,6 +34,8 @@ process CELLRANGER_COUNT { def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir -p "${prefix}/outs/" + mkdir -p "${prefix}/outs/filtered_feature_bc_matrix" + mkdir -p "${prefix}/outs/raw_feature_bc_matrix" echo "$prefix" > ${prefix}/outs/fake_file.txt cat <<-END_VERSIONS > versions.yml From 4fc08d2e22a6e1a04e7ad2537509c2c33ef43292 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Mon, 18 Mar 2024 11:38:07 +0000 Subject: [PATCH 4/5] also create fake files in new stub --- modules/nf-core/cellranger/count/main.nf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf index eeea8ccc203..1811d7457ff 100644 --- a/modules/nf-core/cellranger/count/main.nf +++ b/modules/nf-core/cellranger/count/main.nf @@ -37,6 +37,8 @@ process CELLRANGER_COUNT { mkdir -p "${prefix}/outs/filtered_feature_bc_matrix" mkdir -p "${prefix}/outs/raw_feature_bc_matrix" echo "$prefix" > ${prefix}/outs/fake_file.txt + echo "$prefix" > ${prefix}/outs/filtered_feature_bc_matrix/fake_file.txt + echo "$prefix" > ${prefix}/outs/raw_feature_bc_matrix/fake_file.txt cat <<-END_VERSIONS > versions.yml "${task.process}": From a7ce9683f0f2b2f344eeffd1b80243b32aed842a Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Mon, 18 Mar 2024 11:42:09 +0000 Subject: [PATCH 5/5] update stub snaps as new output channels are now emitted --- .../cellranger/count/tests/main.nf.test.snap | 52 ++++++++++++++++++- 1 file changed, 50 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/cellranger/count/tests/main.nf.test.snap b/modules/nf-core/cellranger/count/tests/main.nf.test.snap index 7eafafd02e9..edfb304b733 100644 --- a/modules/nf-core/cellranger/count/tests/main.nf.test.snap +++ b/modules/nf-core/cellranger/count/tests/main.nf.test.snap @@ -33,13 +33,61 @@ "single_end": false, "strandedness": "auto" }, - "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d" + [ + "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d", + "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d", + "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d" + ] ] ], "1": [ + [ + { + "id": "test_10x", + "single_end": false, + "strandedness": "auto" + }, + "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d" + ] + ], + "2": [ + [ + { + "id": "test_10x", + "single_end": false, + "strandedness": "auto" + }, + "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d" + ] + ], + "3": [ "versions.yml:md5,30cee1a9146b01c48d9b1db6bbe813b6" ], + "filtered": [ + [ + { + "id": "test_10x", + "single_end": false, + "strandedness": "auto" + }, + "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d" + ] + ], "outs": [ + [ + { + "id": "test_10x", + "single_end": false, + "strandedness": "auto" + }, + [ + "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d", + "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d", + "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d" + ] + ] + ], + "raw": [ [ { "id": "test_10x", @@ -58,6 +106,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-05T17:16:12.322822411" + "timestamp": "2024-03-18T11:41:17.258523741" } } \ No newline at end of file