replaced local juno filepaths with git lfs storage paths and renamed …

…parameters so their meaning is more obvious
mskcc · Aug 4, 2023 · de72cc2 · de72cc2
1 parent ef7ee4c
commit de72cc2
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Showing 4 changed files with 16 additions and 13 deletions.
diff --git a/conf/igenomes.config b/conf/igenomes.config
@@ -33,10 +33,10 @@ params {
                     baits = "${params.targets_base}/${params.genome}/baits/agilent_v4/Agilent_v4_51MB_Human_b37_baits.bed"
                 }
             }
-            genebed = "/juno/work/ccs/pintoa1/metafusion_refs/meta_fusion_bed_generation/v75_gene.bed"
-            info = "/juno/work/ccs/pintoa1/fusion_report/metafusion/MetaFusion/gene_info_20230714.txt"
-            block = "/juno/work/ccs/pintoa1/fusion_report/metafusion/MetaFusion/reference_files/blocklist_breakpoints.bedpe"
-            }
+            metafusion_blocklist = "https://media.githubusercontent.com/media/anoronh4/forte-references/main/GRCh37/blocklist_breakpoints.bedpe"
+            metafusion_gene_bed  = "https://media.githubusercontent.com/media/anoronh4/forte-references/main/GRCh37/v75_gene.bed"
+            metafusion_gene_info = "https://media.githubusercontent.com/media/anoronh4/forte-references/main/GRCh37/gene_info_20230714.txt"
+        }
         'GRCh38' {
             fasta          = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
             gtf            = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
@@ -56,6 +56,9 @@ params {
             arriba_known_fusions   = "/usr/local/var/lib/arriba/known_fusions_hg19_hs37d5_GRCh37_v2.3.0.tsv.gz"
             arriba_protein_domains = "/usr/local/var/lib/arriba/protein_domains_hg19_hs37d5_GRCh37_v2.3.0.gff3"
             cdna           = "https://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.75.cdna.all.fa.gz"
+            metafusion_blocklist = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37_test/blocklist_breakpoints.bedpe"
+            metafusion_gene_bed  = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37_test/v75_gene.bed"
+            metafusion_gene_info = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37_test/gene_info_20230714.txt"
 
         }
 /*

diff --git a/main.nf b/main.nf
@@ -24,9 +24,9 @@ params.cdna           = WorkflowMain.getGenomeAttribute(params, 'cdna')
 params.arriba_blacklist       = WorkflowMain.getGenomeAttribute(params, 'arriba_blacklist')
 params.arriba_known_fusions   = WorkflowMain.getGenomeAttribute(params, 'arriba_known_fusions')
 params.arriba_protein_domains = WorkflowMain.getGenomeAttribute(params, 'arriba_protein_domains')
-params.blocklist       = WorkflowMain.getGenomeAttribute(params, 'block')
-params.genebed  = WorkflowMain.getGenomeAttribute(params, 'genebed')
-params.info = WorkflowMain.getGenomeAttribute(params, 'info')
+params.metafusion_blocklist = WorkflowMain.getGenomeAttribute(params, 'metafusion_blocklist')
+params.metafusion_gene_bed  = WorkflowMain.getGenomeAttribute(params, 'metafusion_gene_bed')
+params.metafusion_gene_info = WorkflowMain.getGenomeAttribute(params, 'metafusion_gene_info')
 
 WorkflowMain.initialise(workflow, params, log)
 

diff --git a/subworkflows/local/fusion.nf b/subworkflows/local/fusion.nf
@@ -26,9 +26,9 @@ workflow FUSION {
     main:
     ch_versions = Channel.empty()
     fasta = params.fasta
-    genebed = params.genebed
-    info = params.info
-    blocklist = params.blocklist
+    gene_bed = params.metafusion_gene_bed
+    gene_info = params.metafusion_gene_info
+    blocklist = params.metafusion_blocklist
     numtools = params.numtools
 
     STAR_FOR_ARRIBA(
@@ -101,8 +101,8 @@ workflow FUSION {
 
     METAFUSION(
         MERGE_CFF.out.csv,
-        genebed,
-        info,
+        gene_bed,
+        gene_info,
         fasta,
         blocklist,
         numtools

diff --git a/workflows/forte.nf b/workflows/forte.nf
@@ -10,7 +10,7 @@ def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 WorkflowForte.initialise(params, log)
 
 // Check input path parameters to see if they exist
-def checkPathParamList = [ params.input, params.multiqc_config, params.fasta, params.gtf, params.refflat, params.starfusion_url, params.genebed,params.blocklist,params.info ]
+def checkPathParamList = [ params.input, params.multiqc_config, params.fasta, params.gtf, params.refflat, params.starfusion_url, params.metafusion_gene_bed, params.metafusion_blocklist, params.metafusion_gene_info ]
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
 
 // Check mandatory parameters