Merge pull request #64 from nf-core/initial-release-review-changes

Apply the third set of reviewer recommendations
nf-core · Jul 11, 2024 · 2f86f87 · 2f86f87
2 parents 1f30f98 + 2e37b30
commit 2f86f87
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Showing 6 changed files with 30 additions and 23 deletions.
diff --git a/conf/hmf_genomes.config b/conf/hmf_genomes.config
@@ -10,20 +10,20 @@
 params {
     genomes {
         'GRCh37_hmf' {
-            fasta         = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/Homo_sapiens.GRCh37.GATK.illumina.fasta"
-            fai           = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/samtools_index/1.16/Homo_sapiens.GRCh37.GATK.illumina.fasta.fai"
-            dict          = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/samtools_index/1.16/Homo_sapiens.GRCh37.GATK.illumina.fasta.dict"
-            bwamem2_index = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.1/bwa-mem2_index/2.2.1.tar.gz"
-            gridss_index  = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.1/gridss_index/2.13.2.tar.gz"
-            star_index    = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/star_index/gencode_19/2.7.3a.tar.gz"
+            fasta         = "${params.hmf_genome_base}/GRCh37_hmf/24.0/Homo_sapiens.GRCh37.GATK.illumina.fasta"
+            fai           = "${params.hmf_genome_base}/GRCh37_hmf/24.0/samtools_index/1.16/Homo_sapiens.GRCh37.GATK.illumina.fasta.fai"
+            dict          = "${params.hmf_genome_base}/GRCh37_hmf/24.0/samtools_index/1.16/Homo_sapiens.GRCh37.GATK.illumina.fasta.dict"
+            bwamem2_index = "${params.hmf_genome_base}/GRCh37_hmf/24.1/bwa-mem2_index/2.2.1.tar.gz"
+            gridss_index  = "${params.hmf_genome_base}/GRCh37_hmf/24.1/gridss_index/2.13.2.tar.gz"
+            star_index    = "${params.hmf_genome_base}/GRCh37_hmf/24.0/star_index/gencode_19/2.7.3a.tar.gz"
         }
         'GRCh38_hmf' {
-            fasta         = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
-            fai           = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/samtools_index/1.16/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai"
-            dict          = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/samtools_index/1.16/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.dict"
-            bwamem2_index = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.1/bwa-mem2_index/2.2.1.tar.gz"
-            gridss_index  = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.1/gridss_index/2.13.2.tar.gz"
-            star_index    = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/star_index/gencode_38/2.7.3a.tar.gz"
+            fasta         = "${params.hmf_genome_base}/GRCh38_hmf/24.0/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
+            fai           = "${params.hmf_genome_base}/GRCh38_hmf/24.0/samtools_index/1.16/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai"
+            dict          = "${params.hmf_genome_base}/GRCh38_hmf/24.0/samtools_index/1.16/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.dict"
+            bwamem2_index = "${params.hmf_genome_base}/GRCh38_hmf/24.1/bwa-mem2_index/2.2.1.tar.gz"
+            gridss_index  = "${params.hmf_genome_base}/GRCh38_hmf/24.1/gridss_index/2.13.2.tar.gz"
+            star_index    = "${params.hmf_genome_base}/GRCh38_hmf/24.0/star_index/gencode_38/2.7.3a.tar.gz"
         }
     }
 }
diff --git a/conf/targeted_parameters.config b/conf/targeted_parameters.config
@@ -1,8 +1,14 @@
-process.'withName:^.*:COBALT_PROFILING:COBALT'.ext.args = '-pcf_gamma 50'
+process {
+    withName: '^.*COBALT_PROFILING:COBALT' {
+        ext.args = '-pcf_gamma 50'
+    }
 
-process.'withName:^.*:SAGE_CALLING:SOMATIC'.ext.args = [
-    '-high_depth_mode',
-    '-hard_min_tumor_vaf 0.002',
-    '-hotspot_min_tumor_vaf 0.015',
-    '-panel_min_tumor_qual 150',
-].join(' ').trim()
+    withName: '^.*:SAGE_CALLING:SOMATIC' {
+        ext.args = [
+            '-high_depth_mode',
+            '-hard_min_tumor_vaf 0.002',
+            '-hotspot_min_tumor_vaf 0.015',
+            '-panel_min_tumor_qual 150',
+        ].join(' ').trim()
+    }
+}
diff --git a/nextflow.config b/nextflow.config
@@ -25,6 +25,7 @@ params {
     force_genome    = false
     igenomes_base   = 's3://ngi-igenomes/igenomes'
     igenomes_ignore = true
+    hmf_genome_base = 'https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes'
 
     // Other reference data and config exposed to user on CLI
     max_fastq_records        = 10000000
@@ -73,6 +74,7 @@ params {
         'genome_type',
         'genome_version',
         'genomes',
+        'hmf_genome_base',
         'hmf_data_paths',
         'panel',
         'panel_data_paths',

diff --git a/subworkflows/local/sage_calling/main.nf b/subworkflows/local/sage_calling/main.nf
@@ -20,8 +20,8 @@ workflow SAGE_CALLING {
     genome_version               // channel: [mandatory] genome version
     genome_fai                   // channel: [mandatory] /path/to/genome_fai
     genome_dict                  // channel: [mandatory] /path/to/genome_dict
-    sage_known_hotspots_germline // channel: [optional]  /path/to/sage_known_hotspots_germline
     sage_known_hotspots_somatic  // channel: [mandatory] /path/to/sage_known_hotspots_somatic
+    sage_known_hotspots_germline // channel: [optional]  /path/to/sage_known_hotspots_germline
     sage_actionable_panel        // channel: [mandatory] /path/to/sage_actionable_panel
     sage_coverage_panel          // channel: [mandatory] /path/to/sage_coverage_panel
     sage_highconf_regions        // channel: [mandatory] /path/to/sage_highconf_regions

diff --git a/workflows/targeted.nf b/workflows/targeted.nf
@@ -148,7 +148,6 @@ workflow TARGETED {
     ch_process_dna_normal_out = Channel.empty()
     if (run_config.stages.markdups) {
 
-        // NOTE(SW/MC): hardcoded for initial testing purposes
         has_umis = run_config.panel.equalsIgnoreCase('tso500')
 
         READ_PROCESSING(
@@ -352,8 +351,8 @@ workflow TARGETED {
             ref_data.genome_version,
             ref_data.genome_fai,
             ref_data.genome_dict,
-            [],  // sage_known_hotspots_germline
             hmf_data.sage_known_hotspots_somatic,
+            [],  // sage_known_hotspots_germline
             panel_data.sage_actionable_panel,
             panel_data.sage_coverage_panel,
             hmf_data.sage_highconf_regions,

diff --git a/workflows/wgts.nf b/workflows/wgts.nf
@@ -356,8 +356,8 @@ workflow WGTS {
             ref_data.genome_version,
             ref_data.genome_fai,
             ref_data.genome_dict,
-            hmf_data.sage_known_hotspots_germline,
             hmf_data.sage_known_hotspots_somatic,
+            hmf_data.sage_known_hotspots_germline,
             hmf_data.sage_actionable_panel,
             hmf_data.sage_coverage_panel,
             hmf_data.sage_highconf_regions,