Apply suggestions from code review

robsyme · web-flow · commit 4b6689b1aa1a · 2023-03-31T11:23:54.000+01:00
We don't need to `import nextflow.Nextflow` inside Nextflow scripts because the methods are already in scope
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
@@ -4,7 +4,6 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-import nextflow.Nextflow
 def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 
 // Validate input parameters
@@ -61,9 +60,9 @@ input_sample = params.build_only_index ? Channel.empty() : extract_csv(file(para
 
 // Fails when wrongfull extension for intervals file
 if (params.wes && !params.step == 'annotate') {
-    if (params.intervals && !params.intervals.endsWith("bed"))  Nextflow.error("Target file specified with `--intervals` must be in BED format for targeted data")
+    if (params.intervals && !params.intervals.endsWith("bed"))  error("Target file specified with `--intervals` must be in BED format for targeted data")
     else log.warn("Intervals file was provided without parameter `--wes`: Pipeline will assume this is Whole-Genome-Sequencing data.")
-} else if (params.intervals && !params.intervals.endsWith("bed") && !params.intervals.endsWith("list")) Nextflow.error("Intervals file must end with .bed, .list, or .interval_list")
+} else if (params.intervals && !params.intervals.endsWith("bed") && !params.intervals.endsWith("list")) error("Intervals file must end with .bed, .list, or .interval_list")
 
 if (params.step == 'mapping' && params.aligner.contains("dragmap") && !(params.skip_tools && params.skip_tools.split(',').contains("baserecalibrator"))) {
     log.warn("DragMap was specified as aligner. Base recalibration is not contained in --skip_tools. It is recommended to skip baserecalibration when using DragMap\nhttps://gatk.broadinstitute.org/hc/en-us/articles/4407897446939--How-to-Run-germline-single-sample-short-variant-discovery-in-DRAGEN-mode")
@@ -72,10 +71,10 @@ if (params.step == 'mapping' && params.aligner.contains("dragmap") && !(params.s
 // Fails or warns when missing files or params for ascat
 if (params.tools && params.tools.split(',').contains('ascat')) {
     if (!params.ascat_alleles) {
-        Nextflow.error("No allele files were provided for running ASCAT. Please provide a zip folder with allele files.")
+        error("No allele files were provided for running ASCAT. Please provide a zip folder with allele files.")
     }
     if (!params.ascat_loci) {
-        Nextflow.error("No loci files were provided for running ASCAT. Please provide a zip folder with loci files.")
+        error("No loci files were provided for running ASCAT. Please provide a zip folder with loci files.")
     }
     if (!params.ascat_loci_gc && !params.ascat_loci_rt) {
         log.warn("No LogRCorrection performed in ASCAT. For LogRCorrection to run, please provide either loci gc files or both loci gc files and loci rt files.")
@@ -102,29 +101,29 @@ if (params.tools && params.tools.split(',').contains('mutect2')) {
 // Warns when missing resources for haplotypecaller
 if (!params.dbsnp && !params.known_indels) {
     if (params.step in ['mapping', 'markduplicates', 'prepare_recalibration', 'recalibrate'] && (!params.skip_tools || (params.skip_tools && !params.skip_tools.split(',').contains('baserecalibrator')))) {
-        Nextflow.error("Base quality score recalibration requires at least one resource file. Please provide at least one of `--dbsnp` or `--known_indels`\nYou can skip this step in the workflow by adding `--skip_tools baserecalibrator` to the command.")
+        error("Base quality score recalibration requires at least one resource file. Please provide at least one of `--dbsnp` or `--known_indels`\nYou can skip this step in the workflow by adding `--skip_tools baserecalibrator` to the command.")
     }
     if (params.tools && params.tools.split(',').contains('haplotypecaller')) {
         log.warn "If Haplotypecaller is specified, without `--dbsnp` or `--known_indels no filtering will be done. For filtering, please provide at least one of `--dbsnp` or `--known_indels`.\nFor more information see FilterVariantTranches (single-sample, default): https://gatk.broadinstitute.org/hc/en-us/articles/5358928898971-FilterVariantTranches\nFor more information see VariantRecalibration (--joint_germline): https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator\nFor more information on GATK Best practice germline variant calling: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-"
     }
 }
 if (params.joint_germline && (!params.tools || !params.tools.split(',').contains('haplotypecaller'))) {
-    Nextflow.error("The Haplotypecaller should be specified as one of the tools when doing joint germline variant calling. (The Haplotypecaller could be specified by adding `--tools haplotypecaller` to the nextflow command.) ")
+    error("The Haplotypecaller should be specified as one of the tools when doing joint germline variant calling. (The Haplotypecaller could be specified by adding `--tools haplotypecaller` to the nextflow command.) ")
 }
 if (params.joint_germline && (!params.dbsnp || !params.known_indels || !params.known_snps || params.no_intervals)) {
     log.warn "If Haplotypecaller is specified, without `--dbsnp`, `--known_snps`, `--known_indels` or the associated resource labels (ie `known_snps_vqsr`), no variant recalibration will be done. For recalibration you must provide all of these resources.\nFor more information see VariantRecalibration: https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator \nJoint germline variant calling also requires intervals in order to genotype the samples. As a result, if `--no_intervals` is set to `true` the joint germline variant calling will not be performed."
 }
 
 // Fails when missing tools for variant_calling or annotate
 if ((params.step == 'variant_calling' || params.step == 'annotate') && !params.tools) {
-    Nextflow.error("Please specify at least one tool when using `--step ${params.step}`.\nhttps://nf-co.re/sarek/parameters#tools")
+    error("Please specify at least one tool when using `--step ${params.step}`.\nhttps://nf-co.re/sarek/parameters#tools")
 }
 
 // Fails when missing sex information for CNV tools
 if (params.tools && (params.tools.split(',').contains('ascat') || params.tools.split(',').contains('controlfreec'))) {
     input_sample.map{
         if (it[0].sex == 'NA' ) {
-            Nextflow.error("Please specify sex information for each sample in your samplesheet when using '--tools' with 'ascat' or 'controlfreec'.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
+            error("Please specify sex information for each sample in your samplesheet when using '--tools' with 'ascat' or 'controlfreec'.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
         }
     }
 }
@@ -1098,7 +1097,7 @@ def extract_csv(csv_file) {
         def line, samplesheet_line_count = 0;
         while ((line = reader.readLine()) != null) {samplesheet_line_count++}
         if (samplesheet_line_count < 2) {
-            Nextflow.error("Samplesheet had less than two lines. The sample sheet must be a csv file with a header, so at least two lines.")
+           error("Samplesheet had less than two lines. The sample sheet must be a csv file with a header, so at least two lines.")
         }
     }
 
@@ -1112,19 +1111,19 @@ def extract_csv(csv_file) {
         .map{ row ->
             if (params.step == "mapping") {
                 if ( !row.lane ) {  // This also handles the case where the lane is left as an empty string
-                    Nextflow.error('The sample sheet should specify a lane for patient "' + row.patient.toString() + '" and sample "' + row.sample.toString() + '".')
+                    error('The sample sheet should specify a lane for patient "' + row.patient.toString() + '" and sample "' + row.sample.toString() + '".')
                 }
                 def patient_sample_lane = [row.patient.toString(), row.sample.toString(), row.lane.toString()]
                 if (patient_sample_lane in patient_sample_lane_combinations) {
-                    Nextflow.error('The patient-sample-lane combination "' + row.patient.toString() + '", "' + row.sample.toString() + '", and "' + row.lane.toString() + '" is present multiple times in the sample sheet.')
+                    error('The patient-sample-lane combination "' + row.patient.toString() + '", "' + row.sample.toString() + '", and "' + row.lane.toString() + '" is present multiple times in the sample sheet.')
                 } else {
                     patient_sample_lane_combinations.add(patient_sample_lane)
                 }
             }
             if (!sample2patient.containsKey(row.sample.toString())) {
                 sample2patient[row.sample.toString()] = row.patient.toString()
             } else if (sample2patient[row.sample.toString()] != row.patient.toString()) {
-                Nextflow.error('The sample "' + row.sample.toString() + '" is registered for both patient "' + row.patient.toString() + '" and "' + sample2patient[row.sample.toString()] + '" in the sample sheet.')
+               error('The sample "' + row.sample.toString() + '" is registered for both patient "' + row.patient.toString() + '" and "' + sample2patient[row.sample.toString()] + '" in the sample sheet.')
             }
         }
 
@@ -1137,10 +1136,10 @@ def extract_csv(csv_file) {
         .map{ row ->
             sample_count_all++
             if (!(row.patient && row.sample)) {
-                Nextflow.error("Missing field in csv file header. The csv file must have fields named 'patient' and 'sample'.")
+                error("Missing field in csv file header. The csv file must have fields named 'patient' and 'sample'.")
             }
             else if (row.patient.contains(" ") || row.sample.contains(" ")) {
-                Nextflow.error("Invalid value in csv file. Values for 'patient' and 'sample' can not contain space.")
+                error("Invalid value in csv file. Values for 'patient' and 'sample' can not contain space.")
             }
             [ [ row.patient.toString(), row.sample.toString() ], row ]
         }.groupTuple()
@@ -1181,7 +1180,7 @@ def extract_csv(csv_file) {
                 if (params.tools.split(',').contains(tool)) tools_tumor_asked.add(tool)
             }
             if (!tools_tumor_asked.isEmpty()) {
-                Nextflow.error('The sample-sheet only contains normal-samples, but the following tools, which were requested with "--tools", expect at least one tumor-sample : ' + tools_tumor_asked.join(", "))
+                error('The sample-sheet only contains normal-samples, but the following tools, which were requested with "--tools", expect at least one tumor-sample : ' + tools_tumor_asked.join(", "))
             }
         } else if ((sample_count_tumor == sample_count_all) && params.tools) {  // In this case, the sample-sheet contains no normal/germline-samples
             def tools_requiring_normal_samples = ['ascat', 'deepvariant', 'haplotypecaller', 'msisensorpro']
@@ -1190,7 +1189,7 @@ def extract_csv(csv_file) {
                 if (params.tools.split(',').contains(tool_requiring_normal_samples)) requested_tools_requiring_normal_samples.add(tool_requiring_normal_samples)
             }
             if (!requested_tools_requiring_normal_samples.isEmpty()) {
-                Nextflow.error('The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : ' + requested_tools_requiring_normal_samples.join(", "))
+                error('The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : ' + requested_tools_requiring_normal_samples.join(", "))
             }
         }
 
@@ -1213,13 +1212,13 @@ def extract_csv(csv_file) {
 
             if (params.step == 'mapping') return [ meta, [ fastq_1, fastq_2 ] ]
             else {
-                Nextflow.error("Samplesheet contains fastq files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
+                error("Samplesheet contains fastq files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
             }
 
         // start from BAM
         } else if (row.lane && row.bam) {
             if (!row.bai) {
-                Nextflow.error("BAM index (bai) should be provided.")
+                error("BAM index (bai) should be provided.")
             }
             meta.id         = "${row.sample}-${row.lane}".toString()
             def bam         = file(row.bam,   checkIfExists: true)
@@ -1235,7 +1234,7 @@ def extract_csv(csv_file) {
 
             if (params.step != 'annotate') return [ meta, bam, bai ]
             else {
-                Nextflow.error("Samplesheet contains bam files but step is `annotate`. The pipeline is expecting vcf files for the annotation. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
+                error("Samplesheet contains bam files but step is `annotate`. The pipeline is expecting vcf files for the annotation. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
             }
 
         // recalibration
@@ -1249,7 +1248,7 @@ def extract_csv(csv_file) {
 
             if (!(params.step == 'mapping' || params.step == 'annotate')) return [ meta, cram, crai, table ]
             else {
-                Nextflow.error("Samplesheet contains cram files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
+                error("Samplesheet contains cram files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
             }
 
         // recalibration when skipping MarkDuplicates
@@ -1263,7 +1262,7 @@ def extract_csv(csv_file) {
 
             if (!(params.step == 'mapping' || params.step == 'annotate')) return [ meta, bam, bai, table ]
             else {
-                Nextflow.error("Samplesheet contains bam files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
+                error("Samplesheet contains bam files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
             }
 
         // prepare_recalibration or variant_calling
@@ -1276,7 +1275,7 @@ def extract_csv(csv_file) {
 
             if (!(params.step == 'mapping' || params.step == 'annotate')) return [ meta, cram, crai ]
             else {
-                Nextflow.error("Samplesheet contains cram files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
+                error("Samplesheet contains cram files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
             }
 
         // prepare_recalibration when skipping MarkDuplicates or `--step markduplicates`
@@ -1289,7 +1288,7 @@ def extract_csv(csv_file) {
 
             if (!(params.step == 'mapping' || params.step == 'annotate')) return [ meta, bam, bai ]
             else {
-                Nextflow.error("Samplesheet contains bam files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
+                error("Samplesheet contains bam files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
             }
 
         // annotation
@@ -1302,10 +1301,10 @@ def extract_csv(csv_file) {
 
             if (params.step == 'annotate') return [ meta, vcf ]
             else {
-                Nextflow.error("Samplesheet contains vcf files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
+                error("Samplesheet contains vcf files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
             }
         } else {
-            Nextflow.error("Missing or unknown field in csv file header. Please check your samplesheet")
+            error("Missing or unknown field in csv file header. Please check your samplesheet")
         }
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -4,7 +4,6 @@`
`4`	`4`	`~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~`
`5`	`5`	`*/`
`6`	`6`
`7`		`-import nextflow.Nextflow`
`8`	`7`	`def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)`
`9`	`8`
`10`	`9`	`// Validate input parameters`
`@@ -61,9 +60,9 @@ input_sample = params.build_only_index ? Channel.empty() : extract_csv(file(para`
`61`	`60`
`62`	`61`	`// Fails when wrongfull extension for intervals file`
`63`	`62`	`if (params.wes && !params.step == 'annotate') {`
`64`		- if (params.intervals && !params.intervals.endsWith("bed")) Nextflow.error("Target file specified with `--intervals` must be in BED format for targeted data")
	`63`	+ if (params.intervals && !params.intervals.endsWith("bed")) error("Target file specified with `--intervals` must be in BED format for targeted data")
`65`	`64`	else log.warn("Intervals file was provided without parameter `--wes`: Pipeline will assume this is Whole-Genome-Sequencing data.")
`66`		`-} else if (params.intervals && !params.intervals.endsWith("bed") && !params.intervals.endsWith("list")) Nextflow.error("Intervals file must end with .bed, .list, or .interval_list")`
	`65`	`+} else if (params.intervals && !params.intervals.endsWith("bed") && !params.intervals.endsWith("list")) error("Intervals file must end with .bed, .list, or .interval_list")`
`67`	`66`
`68`	`67`	`if (params.step == 'mapping' && params.aligner.contains("dragmap") && !(params.skip_tools && params.skip_tools.split(',').contains("baserecalibrator"))) {`
`69`	`68`	`log.warn("DragMap was specified as aligner. Base recalibration is not contained in --skip_tools. It is recommended to skip baserecalibration when using DragMap\nhttps://gatk.broadinstitute.org/hc/en-us/articles/4407897446939--How-to-Run-germline-single-sample-short-variant-discovery-in-DRAGEN-mode")`
`@@ -72,10 +71,10 @@ if (params.step == 'mapping' && params.aligner.contains("dragmap") && !(params.s`
`72`	`71`	`// Fails or warns when missing files or params for ascat`
`73`	`72`	`if (params.tools && params.tools.split(',').contains('ascat')) {`
`74`	`73`	`if (!params.ascat_alleles) {`
`75`		`- Nextflow.error("No allele files were provided for running ASCAT. Please provide a zip folder with allele files.")`
	`74`	`+ error("No allele files were provided for running ASCAT. Please provide a zip folder with allele files.")`
`76`	`75`	`}`
`77`	`76`	`if (!params.ascat_loci) {`
`78`		`- Nextflow.error("No loci files were provided for running ASCAT. Please provide a zip folder with loci files.")`
	`77`	`+ error("No loci files were provided for running ASCAT. Please provide a zip folder with loci files.")`
`79`	`78`	`}`
`80`	`79`	`if (!params.ascat_loci_gc && !params.ascat_loci_rt) {`
`81`	`80`	`log.warn("No LogRCorrection performed in ASCAT. For LogRCorrection to run, please provide either loci gc files or both loci gc files and loci rt files.")`
`@@ -102,29 +101,29 @@ if (params.tools && params.tools.split(',').contains('mutect2')) {`
`102`	`101`	`// Warns when missing resources for haplotypecaller`
`103`	`102`	`if (!params.dbsnp && !params.known_indels) {`
`104`	`103`	`if (params.step in ['mapping', 'markduplicates', 'prepare_recalibration', 'recalibrate'] && (!params.skip_tools \|\| (params.skip_tools && !params.skip_tools.split(',').contains('baserecalibrator')))) {`
`105`		- Nextflow.error("Base quality score recalibration requires at least one resource file. Please provide at least one of `--dbsnp` or `--known_indels`\nYou can skip this step in the workflow by adding `--skip_tools baserecalibrator` to the command.")
	`104`	+ error("Base quality score recalibration requires at least one resource file. Please provide at least one of `--dbsnp` or `--known_indels`\nYou can skip this step in the workflow by adding `--skip_tools baserecalibrator` to the command.")
`106`	`105`	`}`
`107`	`106`	`if (params.tools && params.tools.split(',').contains('haplotypecaller')) {`
`108`	`107`	log.warn "If Haplotypecaller is specified, without `--dbsnp` or `--known_indels no filtering will be done. For filtering, please provide at least one of `--dbsnp` or `--known_indels`.\nFor more information see FilterVariantTranches (single-sample, default): https://gatk.broadinstitute.org/hc/en-us/articles/5358928898971-FilterVariantTranches\nFor more information see VariantRecalibration (--joint_germline): https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator\nFor more information on GATK Best practice germline variant calling: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-"
`109`	`108`	`}`
`110`	`109`	`}`
`111`	`110`	`if (params.joint_germline && (!params.tools \|\| !params.tools.split(',').contains('haplotypecaller'))) {`
`112`		- Nextflow.error("The Haplotypecaller should be specified as one of the tools when doing joint germline variant calling. (The Haplotypecaller could be specified by adding `--tools haplotypecaller` to the nextflow command.) ")
	`111`	+ error("The Haplotypecaller should be specified as one of the tools when doing joint germline variant calling. (The Haplotypecaller could be specified by adding `--tools haplotypecaller` to the nextflow command.) ")
`113`	`112`	`}`
`114`	`113`	`if (params.joint_germline && (!params.dbsnp \|\| !params.known_indels \|\| !params.known_snps \|\| params.no_intervals)) {`
`115`	`114`	log.warn "If Haplotypecaller is specified, without `--dbsnp`, `--known_snps`, `--known_indels` or the associated resource labels (ie `known_snps_vqsr`), no variant recalibration will be done. For recalibration you must provide all of these resources.\nFor more information see VariantRecalibration: https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator \nJoint germline variant calling also requires intervals in order to genotype the samples. As a result, if `--no_intervals` is set to `true` the joint germline variant calling will not be performed."
`116`	`115`	`}`
`117`	`116`
`118`	`117`	`// Fails when missing tools for variant_calling or annotate`
`119`	`118`	`if ((params.step == 'variant_calling' \|\| params.step == 'annotate') && !params.tools) {`
`120`		- Nextflow.error("Please specify at least one tool when using `--step ${params.step}`.\nhttps://nf-co.re/sarek/parameters#tools")
	`119`	+ error("Please specify at least one tool when using `--step ${params.step}`.\nhttps://nf-co.re/sarek/parameters#tools")
`121`	`120`	`}`
`122`	`121`
`123`	`122`	`// Fails when missing sex information for CNV tools`
`124`	`123`	`if (params.tools && (params.tools.split(',').contains('ascat') \|\| params.tools.split(',').contains('controlfreec'))) {`
`125`	`124`	`input_sample.map{`
`126`	`125`	`if (it[0].sex == 'NA' ) {`
`127`		`- Nextflow.error("Please specify sex information for each sample in your samplesheet when using '--tools' with 'ascat' or 'controlfreec'.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")`
	`126`	`+ error("Please specify sex information for each sample in your samplesheet when using '--tools' with 'ascat' or 'controlfreec'.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")`
`128`	`127`	`}`
`129`	`128`	`}`
`130`	`129`	`}`
`@@ -1098,7 +1097,7 @@ def extract_csv(csv_file) {`
`1098`	`1097`	`def line, samplesheet_line_count = 0;`
`1099`	`1098`	`while ((line = reader.readLine()) != null) {samplesheet_line_count++}`
`1100`	`1099`	`if (samplesheet_line_count < 2) {`
`1101`		`- Nextflow.error("Samplesheet had less than two lines. The sample sheet must be a csv file with a header, so at least two lines.")`
	`1100`	`+ error("Samplesheet had less than two lines. The sample sheet must be a csv file with a header, so at least two lines.")`
`1102`	`1101`	`}`
`1103`	`1102`	`}`
`1104`	`1103`
`@@ -1112,19 +1111,19 @@ def extract_csv(csv_file) {`
`1112`	`1111`	`.map{ row ->`
`1113`	`1112`	`if (params.step == "mapping") {`
`1114`	`1113`	`if ( !row.lane ) { // This also handles the case where the lane is left as an empty string`
`1115`		`- Nextflow.error('The sample sheet should specify a lane for patient "' + row.patient.toString() + '" and sample "' + row.sample.toString() + '".')`
	`1114`	`+ error('The sample sheet should specify a lane for patient "' + row.patient.toString() + '" and sample "' + row.sample.toString() + '".')`
`1116`	`1115`	`}`
`1117`	`1116`	`def patient_sample_lane = [row.patient.toString(), row.sample.toString(), row.lane.toString()]`
`1118`	`1117`	`if (patient_sample_lane in patient_sample_lane_combinations) {`
`1119`		`- Nextflow.error('The patient-sample-lane combination "' + row.patient.toString() + '", "' + row.sample.toString() + '", and "' + row.lane.toString() + '" is present multiple times in the sample sheet.')`
	`1118`	`+ error('The patient-sample-lane combination "' + row.patient.toString() + '", "' + row.sample.toString() + '", and "' + row.lane.toString() + '" is present multiple times in the sample sheet.')`
`1120`	`1119`	`} else {`
`1121`	`1120`	`patient_sample_lane_combinations.add(patient_sample_lane)`
`1122`	`1121`	`}`
`1123`	`1122`	`}`
`1124`	`1123`	`if (!sample2patient.containsKey(row.sample.toString())) {`
`1125`	`1124`	`sample2patient[row.sample.toString()] = row.patient.toString()`
`1126`	`1125`	`} else if (sample2patient[row.sample.toString()] != row.patient.toString()) {`
`1127`		`- Nextflow.error('The sample "' + row.sample.toString() + '" is registered for both patient "' + row.patient.toString() + '" and "' + sample2patient[row.sample.toString()] + '" in the sample sheet.')`
	`1126`	`+ error('The sample "' + row.sample.toString() + '" is registered for both patient "' + row.patient.toString() + '" and "' + sample2patient[row.sample.toString()] + '" in the sample sheet.')`
`1128`	`1127`	`}`
`1129`	`1128`	`}`
`1130`	`1129`
`@@ -1137,10 +1136,10 @@ def extract_csv(csv_file) {`
`1137`	`1136`	`.map{ row ->`
`1138`	`1137`	`sample_count_all++`
`1139`	`1138`	`if (!(row.patient && row.sample)) {`
`1140`		`- Nextflow.error("Missing field in csv file header. The csv file must have fields named 'patient' and 'sample'.")`
	`1139`	`+ error("Missing field in csv file header. The csv file must have fields named 'patient' and 'sample'.")`
`1141`	`1140`	`}`
`1142`	`1141`	`else if (row.patient.contains(" ") \|\| row.sample.contains(" ")) {`
`1143`		`- Nextflow.error("Invalid value in csv file. Values for 'patient' and 'sample' can not contain space.")`
	`1142`	`+ error("Invalid value in csv file. Values for 'patient' and 'sample' can not contain space.")`
`1144`	`1143`	`}`
`1145`	`1144`	`[ [ row.patient.toString(), row.sample.toString() ], row ]`
`1146`	`1145`	`}.groupTuple()`
`@@ -1181,7 +1180,7 @@ def extract_csv(csv_file) {`
`1181`	`1180`	`if (params.tools.split(',').contains(tool)) tools_tumor_asked.add(tool)`
`1182`	`1181`	`}`
`1183`	`1182`	`if (!tools_tumor_asked.isEmpty()) {`
`1184`		`- Nextflow.error('The sample-sheet only contains normal-samples, but the following tools, which were requested with "--tools", expect at least one tumor-sample : ' + tools_tumor_asked.join(", "))`
	`1183`	`+ error('The sample-sheet only contains normal-samples, but the following tools, which were requested with "--tools", expect at least one tumor-sample : ' + tools_tumor_asked.join(", "))`
`1185`	`1184`	`}`
`1186`	`1185`	`} else if ((sample_count_tumor == sample_count_all) && params.tools) { // In this case, the sample-sheet contains no normal/germline-samples`
`1187`	`1186`	`def tools_requiring_normal_samples = ['ascat', 'deepvariant', 'haplotypecaller', 'msisensorpro']`
`@@ -1190,7 +1189,7 @@ def extract_csv(csv_file) {`
`1190`	`1189`	`if (params.tools.split(',').contains(tool_requiring_normal_samples)) requested_tools_requiring_normal_samples.add(tool_requiring_normal_samples)`
`1191`	`1190`	`}`
`1192`	`1191`	`if (!requested_tools_requiring_normal_samples.isEmpty()) {`
`1193`		`- Nextflow.error('The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : ' + requested_tools_requiring_normal_samples.join(", "))`
	`1192`	`+ error('The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : ' + requested_tools_requiring_normal_samples.join(", "))`
`1194`	`1193`	`}`
`1195`	`1194`	`}`
`1196`	`1195`
`@@ -1213,13 +1212,13 @@ def extract_csv(csv_file) {`
`1213`	`1212`
`1214`	`1213`	`if (params.step == 'mapping') return [ meta, [ fastq_1, fastq_2 ] ]`
`1215`	`1214`	`else {`
`1216`		- Nextflow.error("Samplesheet contains fastq files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
	`1215`	+ error("Samplesheet contains fastq files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
`1217`	`1216`	`}`
`1218`	`1217`
`1219`	`1218`	`// start from BAM`
`1220`	`1219`	`} else if (row.lane && row.bam) {`
`1221`	`1220`	`if (!row.bai) {`
`1222`		`- Nextflow.error("BAM index (bai) should be provided.")`
	`1221`	`+ error("BAM index (bai) should be provided.")`
`1223`	`1222`	`}`
`1224`	`1223`	`meta.id = "${row.sample}-${row.lane}".toString()`
`1225`	`1224`	`def bam = file(row.bam, checkIfExists: true)`
`@@ -1235,7 +1234,7 @@ def extract_csv(csv_file) {`
`1235`	`1234`
`1236`	`1235`	`if (params.step != 'annotate') return [ meta, bam, bai ]`
`1237`	`1236`	`else {`
`1238`		- Nextflow.error("Samplesheet contains bam files but step is `annotate`. The pipeline is expecting vcf files for the annotation. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
	`1237`	+ error("Samplesheet contains bam files but step is `annotate`. The pipeline is expecting vcf files for the annotation. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
`1239`	`1238`	`}`
`1240`	`1239`
`1241`	`1240`	`// recalibration`
`@@ -1249,7 +1248,7 @@ def extract_csv(csv_file) {`
`1249`	`1248`
`1250`	`1249`	`if (!(params.step == 'mapping' \|\| params.step == 'annotate')) return [ meta, cram, crai, table ]`
`1251`	`1250`	`else {`
`1252`		- Nextflow.error("Samplesheet contains cram files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
	`1251`	+ error("Samplesheet contains cram files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
`1253`	`1252`	`}`
`1254`	`1253`
`1255`	`1254`	`// recalibration when skipping MarkDuplicates`
`@@ -1263,7 +1262,7 @@ def extract_csv(csv_file) {`
`1263`	`1262`
`1264`	`1263`	`if (!(params.step == 'mapping' \|\| params.step == 'annotate')) return [ meta, bam, bai, table ]`
`1265`	`1264`	`else {`
`1266`		- Nextflow.error("Samplesheet contains bam files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
	`1265`	+ error("Samplesheet contains bam files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
`1267`	`1266`	`}`
`1268`	`1267`
`1269`	`1268`	`// prepare_recalibration or variant_calling`
`@@ -1276,7 +1275,7 @@ def extract_csv(csv_file) {`
`1276`	`1275`
`1277`	`1276`	`if (!(params.step == 'mapping' \|\| params.step == 'annotate')) return [ meta, cram, crai ]`
`1278`	`1277`	`else {`
`1279`		- Nextflow.error("Samplesheet contains cram files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
	`1278`	+ error("Samplesheet contains cram files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
`1280`	`1279`	`}`
`1281`	`1280`
`1282`	`1281`	// prepare_recalibration when skipping MarkDuplicates or `--step markduplicates`
`@@ -1289,7 +1288,7 @@ def extract_csv(csv_file) {`
`1289`	`1288`
`1290`	`1289`	`if (!(params.step == 'mapping' \|\| params.step == 'annotate')) return [ meta, bam, bai ]`
`1291`	`1290`	`else {`
`1292`		- Nextflow.error("Samplesheet contains bam files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
	`1291`	+ error("Samplesheet contains bam files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
`1293`	`1292`	`}`
`1294`	`1293`
`1295`	`1294`	`// annotation`
`@@ -1302,10 +1301,10 @@ def extract_csv(csv_file) {`
`1302`	`1301`
`1303`	`1302`	`if (params.step == 'annotate') return [ meta, vcf ]`
`1304`	`1303`	`else {`
`1305`		- Nextflow.error("Samplesheet contains vcf files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
	`1304`	+ error("Samplesheet contains vcf files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
`1306`	`1305`	`}`
`1307`	`1306`	`} else {`
`1308`		`- Nextflow.error("Missing or unknown field in csv file header. Please check your samplesheet")`
	`1307`	`+ error("Missing or unknown field in csv file header. Please check your samplesheet")`
`1309`	`1308`	`}`
`1310`	`1309`	`}`
`1311`	`1310`	`}`