Merge pull request #1062 from maxulysse/restart

FIX: automatic restart from step
nf-core · Jun 2, 2023 · 933bddb · 933bddb
2 parents 2848c6d + 0a7b08d
commit 933bddb
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Showing 4 changed files with 16 additions and 13 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -77,6 +77,7 @@ Bierikjávrre is one of the largest lake in Sarek.
 - [#1050](https://github.com/nf-core/sarek/pull/1050) - Disable GATK VCF filters when joint calling to fix [#1025](https://github.com/nf-core/sarek/issues/1025)
 - [#1055](https://github.com/nf-core/sarek/pull/1055) - Fix pattern for fasta file in the json schema
 - [#1058](https://github.com/nf-core/sarek/pull/1058) - Fix container declaration for VCFTOOLS as it has been updated in the registry
+- [#1062](https://github.com/nf-core/sarek/pull/1062) - Fix automatic restart from steps
 
 ### Removed
 

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -84,7 +84,6 @@ class WorkflowMain {
         // Check input has been provided
         if (!params.input && !params.build_only_index) {
             log.warn "No samplesheet specified, attempting to restart from csv files present in ${params.outdir}"
-            WorkflowSarek.retrieveInput(params, log)
         }
     }
     //

diff --git a/lib/WorkflowSarek.groovy b/lib/WorkflowSarek.groovy
@@ -77,29 +77,32 @@ class WorkflowSarek {
     }
 
     public static String retrieveInput(params, log){
-        if (!params.build_only_index) {
+        def input = ''
+        if (params.input) input = params.input
+        else {
             switch (params.step) {
                 case 'mapping':                 Nextflow.error("Can't start with step $params.step without samplesheet")
                                                 break
-                case 'markduplicates':          log.warn("Using file ${params.outdir}/csv/mapped.csv")
-                                                params.putIfAbsent("input","${params.outdir}/csv/mapped.csv");
+                case 'markduplicates':          log.warn("Using file ${params.outdir}/csv/mapped.csv");
+                                                input = params.outdir + "/csv/mapped.csv"
                                                 break
-                case 'prepare_recalibration':   log.warn("Using file ${params.outdir}/csv/markduplicates_no_table.csv")
-                                                params.putIfAbsent("input", "${params.outdir}/csv/markduplicates_no_table.csv");
+                case 'prepare_recalibration':   log.warn("Using file ${params.outdir}/csv/markduplicates_no_table.csv");
+                                                input = params.outdir + "/csv/markduplicates_no_table.csv"
                                                 break
-                case 'recalibrate':             log.warn("Using file ${params.outdir}/csv/markduplicates.csv")
-                                                params.putIfAbsent("input", "${params.outdir}/csv/markduplicates.csv");
+                case 'recalibrate':             log.warn("Using file ${params.outdir}/csv/markduplicates.csv");
+                                                input = params.outdir + "/csv/markduplicates.csv"
                                                 break
-                case 'variant_calling':         log.warn("Using file ${params.outdir}/csv/recalibrated.csv")
-                                                params.putIfAbsent("input", "${params.outdir}/csv/recalibrated.csv");
+                case 'variant_calling':         log.warn("Using file ${params.outdir}/csv/recalibrated.csv");
+                                                input = params.outdir + "/csv/recalibrated.csv"
                                                 break
                 // case 'controlfreec':         csv_file = file("${params.outdir}/variant_calling/csv/control-freec_mpileup.csv", checkIfExists: true); break
-                case 'annotate':                log.warn("Using file ${params.outdir}/csv/variantcalled.csv")
-                                                params.putIfAbsent("input","${params.outdir}/csv/variantcalled.csv");
+                case 'annotate':                log.warn("Using file ${params.outdir}/csv/variantcalled.csv");
+                                                input = params.outdir + "/csv/variantcalled.csv"
                                                 break
                 default:                        log.warn("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'")
                                                 Nextflow.error("Unknown step $params.step")
             }
         }
+        return input
     }
 }
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
@@ -56,7 +56,7 @@ def checkPathParamList = [
 for (param in checkPathParamList) if (param) file(param, checkIfExists: true)
 
 // Set input, can either be from --input or from automatic retrieval in WorkflowSarek.groovy
-input_sample = params.build_only_index ? Channel.empty() : extract_csv(file(params.input, checkIfExists: true))
+input_sample = params.build_only_index ? Channel.empty() : extract_csv(file(WorkflowSarek.retrieveInput(params, log), checkIfExists: true))
 
 // Fails when wrongfull extension for intervals file
 if (params.wes && !params.step == 'annotate') {