@@ -11,14 +11,9 @@ class WorkflowRnaseq {
1111 //
1212 // Check and validate parameters
1313 //
14- public static void initialise (params , log , valid_params ) {
14+ public static void initialise (params , log ) {
1515 genomeExistsError(params, log)
1616
17-
18- if (! params. fasta) {
19- Nextflow . error(" Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
20- }
21-
2217 if (! params. gtf && ! params. gff) {
2318 Nextflow . error(" No GTF or GFF3 annotation specified! The pipeline requires at least one of these files."
2419 }
@@ -54,27 +49,13 @@ class WorkflowRnaseq {
5449 }
5550 }
5651
57- if (! params. skip_trimming) {
58- if (! valid_params[' trimmers' . contains(params. trimmer)) {
59- Nextflow . error(" Invalid option: '${ params.trimmer} ${ valid_params['trimmers'].join(', ')} "
60- }
61- }
62-
63- if (! params. skip_alignment) {
64- if (! valid_params[' aligners' . contains(params. aligner)) {
65- Nextflow . error(" Invalid option: '${ params.aligner} ${ valid_params['aligners'].join(', ')} "
66- }
67- } else {
52+ if (params. skip_alignment) {
6853 skipAlignmentWarn(log)
6954 }
7055
7156 if (! params. skip_pseudo_alignment && params. pseudo_aligner) {
72- if (! valid_params[' pseudoaligners' . contains(params. pseudo_aligner)) {
73- Nextflow . error(" Invalid option: '${ params.pseudo_aligner} ${ valid_params['pseudoaligners'].join(', ')} "
74- } else {
75- if (! (params. salmon_index || params. transcript_fasta || (params. fasta && (params. gtf || params. gff)))) {
76- Nextflow . error(" To use `--pseudo_aligner 'salmon'`, you must provide either --salmon_index or --transcript_fasta or both --fasta and --gtf / --gff."
77- }
57+ if (! (params. salmon_index || params. transcript_fasta || (params. fasta && (params. gtf || params. gff)))) {
58+ Nextflow . error(" To use `--pseudo_aligner 'salmon'`, you must provide either --salmon_index or --transcript_fasta or both --fasta and --gtf / --gff."
7859 }
7960 }
8061
@@ -109,12 +90,34 @@ class WorkflowRnaseq {
10990 }
11091
11192 // Check which RSeQC modules we are running
93+ def valid_rseqc_modules = [' bam_stat' ' inner_distance' ' infer_experiment' ' junction_annotation' ' junction_saturation' ' read_distribution' ' read_duplication' ' tin'
11294 def rseqc_modules = params. rseqc_modules ? params. rseqc_modules. split(' ,' . collect{ it. trim(). toLowerCase() } : []
113- if ((valid_params[ ' rseqc_modules ' ] + rseqc_modules). unique(). size() != valid_params[ ' rseqc_modules ' ] . size()) {
114- Nextflow . error(" Invalid option: ${ params.rseqc_modules} ${ valid_params['rseqc_modules'] .join(', ')} "
95+ if ((valid_rseqc_modules + rseqc_modules). unique(). size() != valid_rseqc_modules . size()) {
96+ Nextflow . error(" Invalid option: ${ params.rseqc_modules} ${ valid_rseqc_modules .join(', ')} "
11597 }
11698 }
11799
100+ //
101+ // Function to validate channels from input samplesheet
102+ //
103+ public static ArrayList validateInput (input ) {
104+ def (metas, fastqs) = input[1 .. 2 ]
105+
106+ // Check that multiple runs of the same sample are of the same strandedness
107+ def strandedness_ok = metas. collect{ it. strandedness }. unique(). size == 1
108+ if (! strandedness_ok) {
109+ Nextflow . error(" Please check input samplesheet -> Multiple runs of a sample must have the same strandedness!: ${ metas[0].id} "
110+ }
111+
112+ // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
113+ def endedness_ok = metas. collect{ it. single_end }. unique(). size == 1
114+ if (! endedness_ok) {
115+ Nextflow . error(" Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${ metas[0].id} "
116+ }
117+
118+ return [ metas[0 ], fastqs ]
119+ }
120+
118121 //
119122 // Function to check whether biotype field exists in GTF file
120123 //
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