From 39d74d460a7883443eaaa0cd515d5c4fa6028905 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Tue, 24 Oct 2023 13:54:27 -0400 Subject: [PATCH 1/4] fix: emit bai file --- modules/CCBR/samtools/sort/main.nf | 6 +++--- .../CCBR/samtools/sort/tests/main.nf.test.snap | 16 ++++++++++------ 2 files changed, 13 insertions(+), 9 deletions(-) diff --git a/modules/CCBR/samtools/sort/main.nf b/modules/CCBR/samtools/sort/main.nf index e12ae37..359b871 100644 --- a/modules/CCBR/samtools/sort/main.nf +++ b/modules/CCBR/samtools/sort/main.nf @@ -8,9 +8,9 @@ process SAMTOOLS_SORT { tuple val(meta), path(bam) output: - tuple val(meta), path("*.bam"), emit: bam - tuple val(meta), path("*.csi"), emit: csi, optional: true - path("versions.yml") , emit: versions + tuple val(meta), path("*.bam"), path("*.bai"), emit: bam + tuple val(meta), path("*.csi"), emit: csi, optional: true + path("versions.yml"), emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/CCBR/samtools/sort/tests/main.nf.test.snap b/modules/CCBR/samtools/sort/tests/main.nf.test.snap index 2ac3593..ce1a093 100644 --- a/modules/CCBR/samtools/sort/tests/main.nf.test.snap +++ b/modules/CCBR/samtools/sort/tests/main.nf.test.snap @@ -8,7 +8,8 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,2488c73846ea4d9cb67187af1c58c716" + "test.sorted.bam:md5,309fd06ed676e7851eda22505132f728", + "test.sorted.bam.bai:md5,2c02a9b519c6979eebf07e3ad40fa12e" ] ], "1": [ @@ -23,7 +24,8 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,2488c73846ea4d9cb67187af1c58c716" + "test.sorted.bam:md5,2488c73846ea4d9cb67187af1c58c716", + "test.sorted.bam.bai:md5,2c02a9b519c6979eebf07e3ad40fa12e" ] ], "csi": [ @@ -34,7 +36,7 @@ ] } ], - "timestamp": "2023-10-24T12:35:29.864751" + "timestamp": "2023-10-24T13:53:20.473892" }, "test_samtools_sort_stub": { "content": [ @@ -45,7 +47,8 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -60,7 +63,8 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "csi": [ @@ -71,6 +75,6 @@ ] } ], - "timestamp": "2023-10-24T12:32:18.504111" + "timestamp": "2023-10-24T13:53:25.129302" } } From 2ced48c97553456cb6145b90574c577c94e1dd90 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Tue, 24 Oct 2023 13:54:54 -0400 Subject: [PATCH 2/4] chore: update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 333c661..a6c80fc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ - khmer/uniquekmers (#7) - picard/samtofastq (#21) - samtools/filteraligned (#13,#20) -- samtools/sort (#24) +- samtools/sort (#24,#28) ### New subworkflows From 9be9a43a28ad75ab1ac1dc008316315585653090 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Tue, 24 Oct 2023 14:06:34 -0400 Subject: [PATCH 3/4] test: fix bai md5sum for gha --- modules/CCBR/samtools/sort/tests/main.nf.test.snap | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/CCBR/samtools/sort/tests/main.nf.test.snap b/modules/CCBR/samtools/sort/tests/main.nf.test.snap index ce1a093..ca365fe 100644 --- a/modules/CCBR/samtools/sort/tests/main.nf.test.snap +++ b/modules/CCBR/samtools/sort/tests/main.nf.test.snap @@ -25,7 +25,7 @@ "single_end": false }, "test.sorted.bam:md5,2488c73846ea4d9cb67187af1c58c716", - "test.sorted.bam.bai:md5,2c02a9b519c6979eebf07e3ad40fa12e" + "test.sorted.bam.bai:md5,be2757b9479e364588d855a77a251940" ] ], "csi": [ From d55ab2580b69a81aa0534a3018cc6e6ea3b28640 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Tue, 24 Oct 2023 14:10:57 -0400 Subject: [PATCH 4/4] test: fix md5sums for both bam and bai --- modules/CCBR/samtools/sort/tests/main.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/CCBR/samtools/sort/tests/main.nf.test.snap b/modules/CCBR/samtools/sort/tests/main.nf.test.snap index ca365fe..bdac18d 100644 --- a/modules/CCBR/samtools/sort/tests/main.nf.test.snap +++ b/modules/CCBR/samtools/sort/tests/main.nf.test.snap @@ -8,8 +8,8 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,309fd06ed676e7851eda22505132f728", - "test.sorted.bam.bai:md5,2c02a9b519c6979eebf07e3ad40fa12e" + "test.sorted.bam:md5,2488c73846ea4d9cb67187af1c58c716", + "test.sorted.bam.bai:md5,be2757b9479e364588d855a77a251940" ] ], "1": [