From 066a55436b9fadd10c8307f106b15f9990206439 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Mon, 1 Jun 2026 13:15:06 +0200 Subject: [PATCH 1/5] update default --- nextflow.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nextflow.config b/nextflow.config index 2266335..f8db398 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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' germline_var_combine = 'all' somatic_var_combine = 'all' - prioritize_caller_germline = 'deepvariant' - prioritize_caller_somatic = 'deepsomatic' + prioritize_caller_germline = 'clair' + prioritize_caller_somatic = 'clair' generate_gvcf = false // Longphase options From 18d322104c06fe71d51048b80ac662da5f0f8cbf Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Mon, 1 Jun 2026 13:31:15 +0200 Subject: [PATCH 2/5] update snap --- tests/default.nf.test.snap | 96 +++++++++----------------------------- 1 file changed, 21 insertions(+), 75 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 8369134..bd126ce 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -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 }, @@ -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, @@ -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, @@ -141,7 +105,7 @@ "whatshap": 2.8 }, "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.1.0" + "IntGenomicsLab/lrsomatic": "v1.1.0dev" } }, [ @@ -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", @@ -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", @@ -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", @@ -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", @@ -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" } } \ No newline at end of file From f7a5797a93cd53e28e518dd7564ecdd8a10bcec3 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Mon, 1 Jun 2026 13:44:55 +0200 Subject: [PATCH 3/5] fix schema --- nextflow_schema.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 57aaecc..ccb3925 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -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", @@ -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": { From 61ad85f3087f519f481d0c0b79bca88fbb0b42b2 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Mon, 1 Jun 2026 13:47:00 +0200 Subject: [PATCH 4/5] no-cert --- conf/modules.config | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index cc3a9e3..9f7d3c3 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -559,6 +559,10 @@ process { } withName : '.*:WGET' { + ext.args = { + [ + "--no-check-certificate" + ].join(' ').trim() } ext.suffix = { "tar.gz" } publishDir = [ enabled: false From dc554c61b4982d52de7481f3678822e87fc92669 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Mon, 1 Jun 2026 15:04:07 +0200 Subject: [PATCH 5/5] update snap --- tests/default.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index bd126ce..c3ba2e3 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -105,7 +105,7 @@ "whatshap": 2.8 }, "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.1.0dev" + "IntGenomicsLab/lrsomatic": "v1.1.0" } }, [ @@ -565,6 +565,6 @@ "nf-test": "0.9.3", "nextflow": "26.04.1" }, - "timestamp": "2026-05-26T13:10:28.130415918" + "timestamp": "2026-06-01T15:01:21.469856129" } } \ No newline at end of file