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Merged
robert-a-forsyth merged 5 commits into from
Jun 1, 2026
Merged

update default #168

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066a554
update default
robert-a-forsyth Jun 1, 2026
18d3221
update snap
robert-a-forsyth Jun 1, 2026
f7a5797
fix schema
robert-a-forsyth Jun 1, 2026
61ad85f
no-cert
robert-a-forsyth Jun 1, 2026
dc554c6
update snap
robert-a-forsyth Jun 1, 2026
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4 changes: 4 additions & 0 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -559,6 +559,10 @@ process {
}

withName : '.*:WGET' {
ext.args = {
[
"--no-check-certificate"
].join(' ').trim() }
ext.suffix = { "tar.gz" }
publishDir = [
enabled: false
Expand Down
8 changes: 4 additions & 4 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -14,12 +14,12 @@ params {
input = null

// Small variant calling options
germline_var_keep = 'deepvariant,clair'
somatic_var_keep = 'deepsomatic,clair'
germline_var_keep = 'clair'
somatic_var_keep = 'clair'
Comment on lines +17 to +18
germline_var_combine = 'all'
somatic_var_combine = 'all'
prioritize_caller_germline = 'deepvariant'
prioritize_caller_somatic = 'deepsomatic'
prioritize_caller_germline = 'clair'
prioritize_caller_somatic = 'clair'
Comment on lines +21 to +22
generate_gvcf = false

// Longphase options
Expand Down
8 changes: 4 additions & 4 deletions nextflow_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -70,12 +70,12 @@
"germline_var_keep": {
"type": "string",
"description": "Comma-separated list of germline variant callers to use. Valid values: deepvariant, clair. Example: 'deepvariant,clair'",
"default": "deepvariant,clair"
"default": "clair"
},
"somatic_var_keep": {
"type": "string",
"description": "Comma-separated list of somatic variant callers to use. Valid values: deepsomatic, clair. Example: 'deepsomatic,clair'",
"default": "deepsomatic,clair"
"default": "clair"
},
"germline_var_combine": {
"type": "string",
Expand All @@ -92,13 +92,13 @@
"prioritize_caller_germline": {
"type": "string",
"description": "When both germline callers are used, specifies which caller's format to use for variants called by both. Must be [deepvariant, clair].",
"default": "deepvariant",
"default": "clair",
"enum": ["deepvariant", "clair"]
},
"prioritize_caller_somatic": {
"type": "string",
"description": "When both somatic callers are used, specifies which caller's format to use for variants called by both. Must be [deepsomatic, clair].",
"default": "deepsomatic",
"default": "clair",
"enum": ["deepsomatic", "clair"]
},
"generate_gvcf": {
Expand Down
96 changes: 21 additions & 75 deletions tests/default.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,21 +2,9 @@
"-profile test": {
"content": [
{
"BCFTOOLS_ANNOTATE": {
"bcftools": 1.22
},
"BCFTOOLS_CONCAT": {
"bcftools": 1.22
},
"BCFTOOLS_ISEC": {
"bcftools": 1.22
},
"BCFTOOLS_NORM": {
"bcftools": 1.22
},
"BCFTOOLS_QUERY": {
"bcftools": 1.22
},
"BCFTOOLS_SORT": {
"bcftools": 1.22
},
Expand All @@ -38,24 +26,6 @@
"CRAMINO_PRE": {
"cramino": "1.3.0"
},
"DEEPSOMATIC_CALLVARIANTS": {
"deepsomatic": "1.7.0"
},
"DEEPSOMATIC_MAKEEXAMPLES": {
"deepsomatic": "1.7.0"
},
"DEEPSOMATIC_POSTPROCESSVARIANTS": {
"deepsomatic": "1.7.0"
},
"DEEPVARIANT_CALLVARIANTS": {
"deepvariant": "1.9.0"
},
"DEEPVARIANT_MAKEEXAMPLES": {
"deepvariant": "1.9.0"
},
"DEEPVARIANT_POSTPROCESSVARIANTS": {
"deepvariant": "1.9.0"
},
"GERMLINE_VEP": {
"ensemblvep": 115.2,
"perl-math-cdf": 0.1,
Expand Down Expand Up @@ -114,12 +84,6 @@
"perl-math-cdf": 0.1,
"tabix": 1.21
},
"SORT_POST_NORM": {
"bcftools": 1.22
},
"STANDARDIZE_AF": {
"bcftools": 1.22
},
"SV_VEP": {
"ensemblvep": 115.2,
"perl-math-cdf": 0.1,
Expand All @@ -141,7 +105,7 @@
"whatshap": 2.8
},
"Workflow": {
"IntGenomicsLab/lrsomatic": "v1.1.0"
"IntGenomicsLab/lrsomatic": "v1.1.0dev"
}
},
[
Expand Down Expand Up @@ -310,12 +274,6 @@
"sample1/variants/clairs/indel.vcf.gz.tbi",
"sample1/variants/clairs/snvs.vcf.gz",
"sample1/variants/clairs/snvs.vcf.gz.tbi",
"sample1/variants/deepsomatic",
"sample1/variants/deepsomatic/sample1_somatic.vcf.gz",
"sample1/variants/deepsomatic/sample1_somatic.vcf.gz.tbi",
"sample1/variants/deepvariant",
"sample1/variants/deepvariant/sample1_germline.vcf.gz",
"sample1/variants/deepvariant/sample1_germline.vcf.gz.tbi",
"sample1/variants/phased",
"sample1/variants/phased/germline_smallvariants.vcf.gz",
"sample1/variants/phased/germline_smallvariants.vcf.gz.tbi",
Expand Down Expand Up @@ -431,12 +389,6 @@
"sample2/variants/clairs/indel.vcf.gz.tbi",
"sample2/variants/clairs/snvs.vcf.gz",
"sample2/variants/clairs/snvs.vcf.gz.tbi",
"sample2/variants/deepsomatic",
"sample2/variants/deepsomatic/sample2_somatic.vcf.gz",
"sample2/variants/deepsomatic/sample2_somatic.vcf.gz.tbi",
"sample2/variants/deepvariant",
"sample2/variants/deepvariant/sample2_germline.vcf.gz",
"sample2/variants/deepvariant/sample2_germline.vcf.gz.tbi",
"sample2/variants/phased",
"sample2/variants/phased/germline_smallvariants.vcf.gz",
"sample2/variants/phased/germline_smallvariants.vcf.gz.tbi",
Expand Down Expand Up @@ -520,12 +472,6 @@
"sample3/variants/clairsto/snv.vcf.gz.tbi",
"sample3/variants/clairsto/somatic.vcf.gz",
"sample3/variants/clairsto/somatic.vcf.gz.tbi",
"sample3/variants/deepsomatic",
"sample3/variants/deepsomatic/sample3_somatic.vcf.gz",
"sample3/variants/deepsomatic/sample3_somatic.vcf.gz.tbi",
"sample3/variants/deepvariant",
"sample3/variants/deepvariant/sample3_germline.vcf.gz",
"sample3/variants/deepvariant/sample3_germline.vcf.gz.tbi",
"sample3/variants/phased",
"sample3/variants/phased/germline_smallvariants.vcf.gz",
"sample3/variants/phased/germline_smallvariants.vcf.gz.tbi",
Expand Down Expand Up @@ -561,52 +507,52 @@
"sample3/vep/somatic/sample3_SOMATIC_VEP.vcf.gz_summary.html"
],
[
"sample1_normal.bam:md5,43e342d8a41b3a408f68ac34a33a2b05",
"sample1_normal.bam.bai:md5,50ae2927e17ecf7c3dca7af48fec9f80",
"sample1_tumor.bam:md5,4fcb482b91f2a2dea52df71933a13b64",
"sample1_tumor.bam.bai:md5,8efbb503e64bf9c779e35f26dc476f61",
"sample1_normal.bam:md5,772e41f7cd86c03a22afbe5ec0592a6b",
"sample1_normal.bam.bai:md5,1b501f6a11efe5d2e6f47b7f1523220b",
"sample1_tumor.bam:md5,c8315c80dc92dfb5d874aef3f5dd46fb",
"sample1_tumor.bam.bai:md5,bc35f807be4b93fc795a14d701469367",
"sample1.flagstat:md5,1c41ea9923945501eb7e41f83a90502d",
"sample1.idxstats:md5,902e503387799123ea59255e3fca172c",
"sample1.stats:md5,a8b3fba9c54efbc0934d6eacc1807140",
"sample1.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf",
"sample1.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93",
"sample1.stats:md5,1c60a1d249d2e503b0678c72e851ea93",
"sample1_whatshap_stats.gtf:md5,428ca0e0f48dc2e3e1b978fa7cf720f3",
"sample1_whatshap_stats.log:md5,5c1f0f79a60a6879b75271fa94b620e8",
"sample1_whatshap_stats.tsv:md5,98582c7e0ff74a2a1978bf70ac9926ee",
"sample1_whatshap_stats.gtf:md5,eff050a68e36e778b06e0ec19435c569",
"sample1_whatshap_stats.log:md5,76b73731f74fe32ef2d11f6bb0a0f71a",
"sample1_whatshap_stats.tsv:md5,f566ae25b3c5a8f7e94b3d6c1b0417f8",
"breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18",
"breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50",
"breakpoints_double.csv:md5,47cb0e0bbe71abdbf4f40217dfda43f9",
"read_qual.txt:md5,78247dfa2ea336eac0e128eba5e9eef4",
"breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18",
"breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50",
"sample2_normal.bam:md5,e6f663652f11e37ef2133cea2c442e67",
"sample2_normal.bam.bai:md5,b9f92cd24a60246f91eeff88e352de92",
"sample2_tumor.bam:md5,ed4b6729c6cdcc0f6b912dd2012bde13",
"sample2_tumor.bam.bai:md5,ceaf4a372036ced03de5bdf0a095a4e0",
"sample2_normal.bam:md5,3157bd11ba095a884c7951aafcfcfb1c",
"sample2_normal.bam.bai:md5,edebda44c4383173caea728acde4ac43",
"sample2_tumor.bam:md5,47b2c5f86e0493ba94ff72cea77eeae3",
"sample2_tumor.bam.bai:md5,abf2c290c815f54c2b3f8179f717d9bd",
"sample2.flagstat:md5,714d0cc0c213e2640e54a16f3d0e6e7e",
"sample2.idxstats:md5,72eb83bb11748dc863fef1a0a5497e4b",
"sample2.stats:md5,20c47cb94f9ac739d69c57be6daf82c5",
"sample2.flagstat:md5,4344a8745efef9cc2a017024218d61c6",
"sample2.idxstats:md5,69467fc02c83a30084736aeea8b785fb",
"sample2.stats:md5,8635df10132c85a13f2d9878b7cf90a2",
"sample2_whatshap_stats.gtf:md5,a13f0ac1edd7abde4ad013bf2619fe0f",
"sample2_whatshap_stats.log:md5,1d5ed1faca328d3014e9b14a44d18a23",
"sample2_whatshap_stats.tsv:md5,a275209ef9e7885ee5ea3a4aa1c970fd",
"sample2_whatshap_stats.gtf:md5,4d8f4393e3aebe4e945c0b8236cf3b3e",
"sample2_whatshap_stats.log:md5,10bba7bae6dd99b989ece5e5dac7a8f9",
"sample2_whatshap_stats.tsv:md5,bb46226e486af9026ab76e014624e903",
"breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18",
"breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50",
"breakpoints_double.csv:md5,48baac86492026a4a7947bc708c47e6e",
"read_qual.txt:md5,8b92ff7dc4536188be159b95525511cd",
"breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18",
"breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50",
"sample3_tumor.bam:md5,4217ff1858357413be33ddec9ee7b609",
"sample3_tumor.bam.bai:md5,44cbd5225d18505b67a24dcf1e830d96",
"sample3_tumor.bam:md5,3c995151bdd974df5bf61d08606d54d3",
"sample3_tumor.bam.bai:md5,9d5964ef8f44127a7d9162d628e2407d",
"sample3.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf",
"sample3.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93",
"sample3.stats:md5,ecd5ea4fee37379dd5c5ae3e89dfddda",
"sample3_whatshap_stats.gtf:md5,415b20e0cc30409d24501d64b185dc49",
"sample3_whatshap_stats.log:md5,99a842c8f8f3259ec66b68e8fe0345e6",
"sample3_whatshap_stats.tsv:md5,a65d179e31756ae4127f0bf74da7e701",
"sample3_whatshap_stats.gtf:md5,46a97067376b06b476d180709bc9e3d8",
"sample3_whatshap_stats.log:md5,376254ec9c98f9ba204895e7085516ed",
"sample3_whatshap_stats.tsv:md5,f7cc79156f23e884ead18e50b8434dbf",
"breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18",
"breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50",
"breakpoints_double.csv:md5,56e899f85876cee082788927d0f89c5f",
Expand All @@ -619,6 +565,6 @@
"nf-test": "0.9.3",
"nextflow": "26.04.1"
},
"timestamp": "2026-05-28T14:16:24.602965551"
"timestamp": "2026-05-26T13:10:28.130415918"
}
}
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