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Fix/automap updio issues #184

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merged 5 commits into from
Aug 8, 2024
Merged

Fix/automap updio issues #184

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566ce0c
edit automap outdir
nvnieuwk Aug 5, 2024
13c1ea4
use sample id for automap individuals
nvnieuwk Aug 5, 2024
ed11b25
remove view statements
nvnieuwk Aug 6, 2024
a2224a2
fix tests
nvnieuwk Aug 6, 2024
7f36cda
update changelog
nvnieuwk Aug 6, 2024
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2 changes: 1 addition & 1 deletion conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -564,7 +564,7 @@ process {
withName: "^.*VCF_ROH_AUTOMAP:AUTOMAP_AUTOMAP\$" {
ext.prefix = {"automap_${meta.caller}"}
ext.args = {[
meta.family_count > 1 ? "--multivcf" : "",
meta.family_count > 1 ? "--multivcf" : "--id ${meta.samples}",
params.automap_panel_name ? "--panelname ${params.automap_panel_name}" : ""
].findAll { it != "" }.join(" ")}
publishDir = [
Expand Down
2 changes: 1 addition & 1 deletion modules/local/automap/automap/main.nf
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Expand Up @@ -29,7 +29,7 @@ process AUTOMAP_AUTOMAP {
automap \\
--vcf $vcf \\
--genome $hg_genome \\
--out $prefix \\
--out $prefix/ \\
--repeats $repeats \\
$panel_file \\
$args
Expand Down
4 changes: 4 additions & 0 deletions subworkflows/local/cram_call_vardictjava/main.nf
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Expand Up @@ -125,6 +125,10 @@ workflow CRAM_CALL_VARDICTJAVA {

ch_filter_output
.join(TABIX_TABIX.out.tbi, failOnDuplicate: true, failOnMismatch: true)
.map { meta, vcf, tbi ->
def new_meta = meta + [samples: meta.sample]
[ new_meta, vcf, tbi ]
}
.set { ch_vcfs }

emit:
Expand Down
12 changes: 10 additions & 2 deletions subworkflows/local/gvcf_joint_genotype_gatk4/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -53,9 +53,13 @@ workflow GVCF_JOINT_GENOTYPE_GATK4 {
family_count: meta.family_count,
caller: meta.caller
]
[ groupKey(new_meta, meta.family_count.toInteger()), gvcf, tbi ]
[ groupKey(new_meta, meta.family_count.toInteger()), gvcf, tbi, meta.sample ]
}
.groupTuple()
.map { meta, gvcf, tbi, samples ->
def new_meta = meta + [samples: "${samples.sort(false).join(',')}"] // Having a comma-separated string ensures that joins don't fail
[ new_meta, gvcf, tbi ]
}
.combine(GAWK.out.output.map { it[1] })
.map { meta, gvcfs, tbis, bed ->
[ meta, gvcfs, tbis, bed, [], [] ]
Expand Down Expand Up @@ -89,9 +93,13 @@ workflow GVCF_JOINT_GENOTYPE_GATK4 {
family_count: meta.family_count,
caller: meta.caller
]
[ groupKey(new_meta, meta.family_count.toInteger()), bed ]
[ groupKey(new_meta, meta.family_count.toInteger()), bed, meta.sample ]
}
.groupTuple()
.map { meta, bed, samples ->
def new_meta = meta + [samples: "${samples.sort(false).join(',')}"] // Having a comma-separated string ensures that joins don't fail
[ new_meta, bed ]
}
.dump(tag:'merge_beds_input', pretty: true)
.set { ch_merge_beds_input }

Expand Down
45 changes: 25 additions & 20 deletions tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap
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Expand Up @@ -24,7 +24,8 @@
"family": "Ashkenazim",
"id": "Ashkenazim",
"family_count": 3,
"caller": "haplotypecaller"
"caller": "haplotypecaller",
"samples": "NA24143,NA24149,NA24835"
},
"Ashkenazim.haplotypecaller.vcf.gz",
"Ashkenazim.haplotypecaller.vcf.gz.tbi"
Expand All @@ -37,10 +38,10 @@
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-03-27T10:07:15.389498873"
"timestamp": "2024-08-06T13:01:36.711373912"
},
"filter - family": {
"content": [
Expand All @@ -50,7 +51,8 @@
"family": "Ashkenazim",
"id": "Ashkenazim",
"family_count": 3,
"caller": "haplotypecaller"
"caller": "haplotypecaller",
"samples": "NA24143,NA24149,NA24835"
},
"Ashkenazim.haplotypecaller.vcf.gz",
"Ashkenazim.haplotypecaller.vcf.gz.tbi"
Expand All @@ -63,10 +65,10 @@
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-03-27T10:11:00.537979751"
"timestamp": "2024-08-06T13:02:26.651064532"
},
"default - gvcfs": {
"content": [
Expand All @@ -76,7 +78,8 @@
"family": "Ashkenazim",
"id": "Ashkenazim",
"family_count": 1,
"caller": "haplotypecaller"
"caller": "haplotypecaller",
"samples": "NA24143"
},
"Ashkenazim.haplotypecaller.vcf.gz",
"Ashkenazim.haplotypecaller.vcf.gz.tbi"
Expand All @@ -87,10 +90,10 @@
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-03-27T10:09:15.858225835"
"timestamp": "2024-08-06T12:56:23.435795439"
},
"default - crams": {
"content": [
Expand All @@ -100,7 +103,8 @@
"family": "Ashkenazim",
"id": "Ashkenazim",
"family_count": 1,
"caller": "haplotypecaller"
"caller": "haplotypecaller",
"samples": "NA24143"
},
"Ashkenazim.haplotypecaller.vcf.gz",
"Ashkenazim.haplotypecaller.vcf.gz.tbi"
Expand All @@ -113,10 +117,10 @@
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-03-27T10:06:11.00007181"
"timestamp": "2024-08-06T12:55:51.608812907"
},
"only_call - family": {
"content": [
Expand All @@ -143,7 +147,8 @@
"family": "Ashkenazim",
"id": "Ashkenazim",
"family_count": 2,
"caller": "haplotypecaller"
"caller": "haplotypecaller",
"samples": "NA24143,NA24835"
},
"Ashkenazim.haplotypecaller.vcf.gz",
"Ashkenazim.haplotypecaller.vcf.gz.tbi"
Expand All @@ -156,9 +161,9 @@
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-03-27T10:22:47.471505664"
"timestamp": "2024-08-06T13:04:20.473178165"
}
}
30 changes: 17 additions & 13 deletions tests/subworkflows/local/cram_call_vardictjava/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8,18 +8,19 @@
"sample": "NA24143",
"family": "Ashkenazim",
"family_count": 1,
"caller": "vardict"
"caller": "vardict",
"samples": "NA24143"
},
"NA24143.vardict.vcf.gz",
"NA24143.vardict.vcf.gz.tbi"
]
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-03-27T10:30:53.553985963"
"timestamp": "2024-08-06T13:05:31.562298546"
},
"default": {
"content": [
Expand All @@ -30,18 +31,19 @@
"sample": "NA24143",
"family": "Ashkenazim",
"family_count": 1,
"caller": "vardict"
"caller": "vardict",
"samples": "NA24143"
},
"NA24143.vardict.vcf.gz",
"NA24143.vardict.vcf.gz.tbi"
]
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-03-27T10:31:27.5084132"
"timestamp": "2024-08-06T13:05:04.322416692"
},
"family": {
"content": [
Expand All @@ -52,7 +54,8 @@
"sample": "NA24143",
"family": "Ashkenazim",
"family_count": 2,
"caller": "vardict"
"caller": "vardict",
"samples": "NA24143"
},
"NA24143.vardict.vcf.gz",
"NA24143.vardict.vcf.gz.tbi"
Expand All @@ -63,17 +66,18 @@
"sample": "NA24149",
"family": "Ashkenazim",
"family_count": 2,
"caller": "vardict"
"caller": "vardict",
"samples": "NA24149"
},
"NA24149.vardict.vcf.gz",
"NA24149.vardict.vcf.gz.tbi"
]
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-03-27T10:33:57.915748864"
"timestamp": "2024-08-06T13:06:05.012625054"
}
}
4 changes: 2 additions & 2 deletions tests/subworkflows/local/vcf_roh_automap/main.nf.test
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Expand Up @@ -18,7 +18,7 @@ nextflow_workflow {
workflow {
"""
input[0] = Channel.of([
[id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller"],
[id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller", samples: "NA24143,NA24835,NA24149"],
file(params.famvcf, checkIfExists:true),
file(params.famtbi, checkIfExists:true)
])
Expand Down Expand Up @@ -58,7 +58,7 @@ nextflow_workflow {
workflow {
"""
input[0] = Channel.of([
[id:"NA24143", family:"NA24143", family_count:1, caller:"haplotypecaller"],
[id:"NA24143", family:"NA24143", family_count:1, caller:"haplotypecaller", samples: "NA24143,NA24835,NA24149"],
file(params.vcf1, checkIfExists:true),
file(params.tbi1, checkIfExists:true)
])
Expand Down
18 changes: 10 additions & 8 deletions tests/subworkflows/local/vcf_roh_automap/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,8 @@
"id": "Ashkenazim",
"family": "Ashkenazim",
"family_count": 3,
"caller": "haplotypecaller"
"caller": "haplotypecaller",
"samples": "NA24143,NA24835,NA24149"
},
[
[
Expand All @@ -24,10 +25,10 @@
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-04-04T16:13:43.925198036"
"timestamp": "2024-08-06T13:06:37.322068108"
},
"default - sample": {
"content": [
Expand All @@ -37,7 +38,8 @@
"id": "NA24143",
"family": "NA24143",
"family_count": 1,
"caller": "haplotypecaller"
"caller": "haplotypecaller",
"samples": "NA24143,NA24835,NA24149"
},
[
"NA24143.HomRegions.cmgg_bio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
Expand All @@ -49,9 +51,9 @@
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-04-04T16:03:23.276826691"
"timestamp": "2024-08-06T13:06:47.205904762"
}
}
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