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fix: Improve samtools flagstat stub to generate realistic output #9064

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Merged
merged 5 commits into from
Sep 15, 2025
Merged

fix: Improve samtools flagstat stub to generate realistic output #9064

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e396813
fix: Improve samtools flagstat stub to generate realistic output
edmundmiller Sep 15, 2025
50f8764
test: Update samtools flagstat snapshots with current versions
edmundmiller Sep 15, 2025
93c5421
test: Update bam_stats_samtools snapshots for improved flagstat stub
edmundmiller Sep 15, 2025
331d8d0
test: Fix samtools flagstat snapshots for CI environment
edmundmiller Sep 15, 2025
e9aa2d9
test: Update bam_stats_samtools snapshots with Docker profile
edmundmiller Sep 15, 2025
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14 changes: 13 additions & 1 deletion modules/nf-core/samtools/flagstat/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,19 @@ process SAMTOOLS_FLAGSTAT {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.flagstat
cat <<-END_FLAGSTAT > ${prefix}.flagstat
1000000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
900000 + 0 mapped (90.00% : N/A)
1000000 + 0 paired in sequencing
500000 + 0 read1
500000 + 0 read2
800000 + 0 properly paired (80.00% : N/A)
850000 + 0 with mate mapped to a different chr
50000 + 0 with mate mapped to a different chr (mapQ>=5)
END_FLAGSTAT

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/samtools/flagstat/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
"id": "test",
"single_end": false
},
"test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
]
],
"1": [
Expand All @@ -20,7 +20,7 @@
"id": "test",
"single_end": false
},
"test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
]
],
"versions": [
Expand All @@ -32,7 +32,7 @@
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-10T13:31:17.098789"
"timestamp": "2025-09-15T15:02:00.813612"
},
"BAM": {
"content": [
Expand Down Expand Up @@ -67,6 +67,6 @@
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-10T13:31:12.661288"
"timestamp": "2025-09-15T15:01:55.232954"
}
}
24 changes: 12 additions & 12 deletions subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
"id": "test",
"single_end": true
},
"test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
]
],
"2": [
Expand All @@ -40,7 +40,7 @@
"id": "test",
"single_end": true
},
"test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
]
],
"idxstats": [
Expand Down Expand Up @@ -72,7 +72,7 @@
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-10T13:37:48.492968"
"timestamp": "2025-09-15T15:20:35.417926"
},
"test_bam_stats_samtools_single_end - stub": {
"content": [
Expand All @@ -92,7 +92,7 @@
"id": "test",
"single_end": true
},
"test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
]
],
"2": [
Expand All @@ -115,7 +115,7 @@
"id": "test",
"single_end": true
},
"test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
]
],
"idxstats": [
Expand Down Expand Up @@ -147,7 +147,7 @@
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-10T13:37:43.4053"
"timestamp": "2025-09-15T15:20:25.439222"
},
"test_bam_stats_samtools_paired_end_cram - stub": {
"content": [
Expand All @@ -167,7 +167,7 @@
"id": "test",
"single_end": false
},
"test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
]
],
"2": [
Expand All @@ -190,7 +190,7 @@
"id": "test",
"single_end": false
},
"test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
]
],
"idxstats": [
Expand Down Expand Up @@ -222,7 +222,7 @@
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-10T13:37:53.52248"
"timestamp": "2025-09-15T15:20:46.02738"
},
"test_bam_stats_samtools_single_end": {
"content": [
Expand Down Expand Up @@ -263,7 +263,7 @@
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-10T13:37:27.672053"
"timestamp": "2025-09-15T15:20:00.064679"
},
"test_bam_stats_samtools_paired_end": {
"content": [
Expand Down Expand Up @@ -304,7 +304,7 @@
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-10T13:37:32.985079"
"timestamp": "2025-09-15T15:20:08.141202"
},
"test_bam_stats_samtools_paired_end_cram": {
"content": [
Expand Down Expand Up @@ -345,6 +345,6 @@
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-10T13:37:38.347584"
"timestamp": "2025-09-15T15:20:16.06318"
}
}
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