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remove redundant .first() operations #769

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Merged
ramprasadn merged 8 commits into from
Jan 24, 2026
Merged

remove redundant .first() operations #769

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e3888fa
remove first in versions
ramprasadn Jan 22, 2026
ed58bb2
Merge branch 'dev' into refactor2
ramprasadn Jan 22, 2026
af12581
update snaps
ramprasadn Jan 23, 2026
a42f5a8
Merge branch 'refactor2' of github.com:nf-core/raredisease into refac…
ramprasadn Jan 23, 2026
9c39972
fix?
ramprasadn Jan 23, 2026
91a992c
[automated] Fix code linting
nf-core-bot Jan 23, 2026
cb61a4f
update snap
ramprasadn Jan 23, 2026
ee60f26
Merge branch 'refactor2' of github.com:nf-core/raredisease into refac…
ramprasadn Jan 23, 2026
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92 changes: 87 additions & 5 deletions subworkflows/local/align/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -239,36 +239,72 @@
],
[
"versions.yml:md5,04cb590a101237e8d8726039ee466819",
"versions.yml:md5,04cb590a101237e8d8726039ee466819",
"versions.yml:md5,04cb590a101237e8d8726039ee466819",
"versions.yml:md5,210790d64830e81c512ff898e8d888db",
"versions.yml:md5,210790d64830e81c512ff898e8d888db",
"versions.yml:md5,210790d64830e81c512ff898e8d888db",
"versions.yml:md5,3524532e0d268745c6d6c785bc7e734e",
"versions.yml:md5,3524532e0d268745c6d6c785bc7e734e",
"versions.yml:md5,3524532e0d268745c6d6c785bc7e734e",
"versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a",
"versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a",
"versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a",
"versions.yml:md5,6cbf152be76b9a14bb7eccb2658cabb3",
"versions.yml:md5,6cbf152be76b9a14bb7eccb2658cabb3",
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"versions.yml:md5,76abbad692af483cd9c6bc9c5d29b330",
"versions.yml:md5,76abbad692af483cd9c6bc9c5d29b330",
"versions.yml:md5,76abbad692af483cd9c6bc9c5d29b330",
"versions.yml:md5,7b799d18a80d6d144122cc97f83748c3",
"versions.yml:md5,7b799d18a80d6d144122cc97f83748c3",
"versions.yml:md5,7b799d18a80d6d144122cc97f83748c3",
"versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9",
"versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9",
"versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9",
"versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5",
"versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5",
"versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5",
"versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e",
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"versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e",
"versions.yml:md5,914929705542ec69faf26ad6c672e2af",
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"versions.yml:md5,9c218b25dd02dc279b1ce6fad9ae182b",
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"versions.yml:md5,b1c46403177c797d5fc304eebf16731c",
"versions.yml:md5,b1c46403177c797d5fc304eebf16731c",
"versions.yml:md5,b1c46403177c797d5fc304eebf16731c",
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"versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec",
"versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec",
"versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec",
"versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f",
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"versions.yml:md5,c31eb465488334212645bd43296d8bd7",
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"versions.yml:md5,d19b223e2ea8c907b23c9b301c15f3fb",
"versions.yml:md5,d19b223e2ea8c907b23c9b301c15f3fb",
"versions.yml:md5,deacbc4b4196d58efb6dab2e2d333ee9",
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"versions.yml:md5,f8dd98ba8455bb8d00379fba39cc9e65"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-12-03T13:44:41.37749287"
"timestamp": "2026-01-23T09:10:54.26947033"
},
"align bwameme - wgs": {
"content": [
Expand Down Expand Up @@ -395,33 +431,69 @@
],
[
"versions.yml:md5,04cb590a101237e8d8726039ee466819",
"versions.yml:md5,04cb590a101237e8d8726039ee466819",
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"versions.yml:md5,f8dd98ba8455bb8d00379fba39cc9e65"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-12-03T17:04:26.065011032"
"timestamp": "2026-01-23T09:19:59.751912776"
},
"align bwamem2 - wes": {
"content": [
Expand Down Expand Up @@ -495,19 +567,29 @@
],
[
"versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a",
"versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a",
"versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a",
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"versions.yml:md5,7b799d18a80d6d144122cc97f83748c3",
"versions.yml:md5,7b799d18a80d6d144122cc97f83748c3",
"versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9",
"versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9",
"versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9",
"versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5",
"versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5",
"versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5",
"versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e",
"versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e",
"versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e",
"versions.yml:md5,c31eb465488334212645bd43296d8bd7",
"versions.yml:md5,c31eb465488334212645bd43296d8bd7",
"versions.yml:md5,c31eb465488334212645bd43296d8bd7"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-12-08T16:34:03.159847454"
"timestamp": "2026-01-23T09:11:40.672538153"
}
}
14 changes: 7 additions & 7 deletions subworkflows/local/align_MT/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,15 +27,15 @@ workflow ALIGN_MT {
if (val_mt_aligner.equals("bwamem2")) {
BWAMEM2_MEM_MT (ch_fastq, ch_bwamem2index, ch_fasta, true)
ch_align = BWAMEM2_MEM_MT.out.bam
ch_versions = ch_versions.mix(BWAMEM2_MEM_MT.out.versions.first())
ch_versions = ch_versions.mix(BWAMEM2_MEM_MT.out.versions)
} else if (val_mt_aligner.equals("sentieon")) {
SENTIEON_BWAMEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, ch_fai )
ch_align = SENTIEON_BWAMEM_MT.out.bam_and_bai.map{ meta, bam, _bai -> [meta, bam] }
ch_versions = ch_versions.mix(SENTIEON_BWAMEM_MT.out.versions.first())
ch_versions = ch_versions.mix(SENTIEON_BWAMEM_MT.out.versions)
} else if (val_mt_aligner.equals("bwa")) {
BWA_MEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, true )
ch_align = BWA_MEM_MT.out.bam
ch_versions = ch_versions.mix(BWA_MEM_MT.out.versions.first())
ch_versions = ch_versions.mix(BWA_MEM_MT.out.versions)
}
ch_align
.join(ch_ubam, failOnMismatch:true, failOnDuplicate:true)
Expand All @@ -49,10 +49,10 @@ workflow ALIGN_MT {

SAMTOOLS_SORT_MT (PICARD_MARKDUPLICATES_MT.out.bam, [[:],[]], 'bai')

ch_versions = ch_versions.mix(GATK4_MERGEBAMALIGNMENT_MT.out.versions.first())
ch_versions = ch_versions.mix(PICARD_ADDORREPLACEREADGROUPS_MT.out.versions.first())
ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES_MT.out.versions.first())
ch_versions = ch_versions.mix(SAMTOOLS_SORT_MT.out.versions.first())
ch_versions = ch_versions.mix(GATK4_MERGEBAMALIGNMENT_MT.out.versions)
ch_versions = ch_versions.mix(PICARD_ADDORREPLACEREADGROUPS_MT.out.versions)
ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES_MT.out.versions)
ch_versions = ch_versions.mix(SAMTOOLS_SORT_MT.out.versions)

emit:
marked_bai = SAMTOOLS_SORT_MT.out.bai // channel: [ val(meta), path(bai) ]
Expand Down
44 changes: 42 additions & 2 deletions subworkflows/local/align_MT/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -104,9 +104,19 @@
],
"2": [
"versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89",
"versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89",
"versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89",
"versions.yml:md5,84869ed38f4bfecb303ea73297f03a04",
"versions.yml:md5,84869ed38f4bfecb303ea73297f03a04",
"versions.yml:md5,84869ed38f4bfecb303ea73297f03a04",
"versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5",
"versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5",
"versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5",
"versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef",
"versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef",
"versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef",
"versions.yml:md5,ee160a842ca6cba016914a1d7a69e970",
"versions.yml:md5,ee160a842ca6cba016914a1d7a69e970",
"versions.yml:md5,ee160a842ca6cba016914a1d7a69e970"
],
"marked_bai": [
Expand Down Expand Up @@ -211,9 +221,19 @@
],
"versions": [
"versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89",
"versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89",
"versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89",
"versions.yml:md5,84869ed38f4bfecb303ea73297f03a04",
"versions.yml:md5,84869ed38f4bfecb303ea73297f03a04",
"versions.yml:md5,84869ed38f4bfecb303ea73297f03a04",
"versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5",
"versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5",
"versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5",
"versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef",
"versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef",
"versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef",
"versions.yml:md5,ee160a842ca6cba016914a1d7a69e970",
"versions.yml:md5,ee160a842ca6cba016914a1d7a69e970",
"versions.yml:md5,ee160a842ca6cba016914a1d7a69e970"
]
}
Expand All @@ -222,7 +242,7 @@
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-12-19T17:12:01.590311293"
"timestamp": "2026-01-23T09:23:15.456518407"
},
"align mt - bwa": {
"content": [
Expand Down Expand Up @@ -329,9 +349,19 @@
],
"2": [
"versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c",
"versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c",
"versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c",
"versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89",
"versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89",
"versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89",
"versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5",
"versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5",
"versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5",
"versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef",
"versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef",
"versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef",
"versions.yml:md5,ee160a842ca6cba016914a1d7a69e970",
"versions.yml:md5,ee160a842ca6cba016914a1d7a69e970",
"versions.yml:md5,ee160a842ca6cba016914a1d7a69e970"
],
"marked_bai": [
Expand Down Expand Up @@ -436,9 +466,19 @@
],
"versions": [
"versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c",
"versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c",
"versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c",
"versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89",
"versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89",
"versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89",
"versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5",
"versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5",
"versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5",
"versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef",
"versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef",
"versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef",
"versions.yml:md5,ee160a842ca6cba016914a1d7a69e970",
"versions.yml:md5,ee160a842ca6cba016914a1d7a69e970",
"versions.yml:md5,ee160a842ca6cba016914a1d7a69e970"
]
}
Expand All @@ -447,6 +487,6 @@
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-12-19T17:14:00.976440705"
"timestamp": "2026-01-23T09:26:33.086288065"
}
}
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