Skip to content

update default #168

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
robert-a-forsyth merged 5 commits into from
Jun 1, 2026
+32 −82
Merged

update default #168

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 4 additions & 0 deletions conf/modules.config
View file
Open in desktop
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
View file
Open in desktop
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
View file
Open in desktop
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
94 changes: 20 additions & 74 deletions tests/default.nf.test.snap
View file
Open in desktop
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 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": "2026-06-01T15:01:21.469856129"
}
}
Loading