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drpatelhdrpatelh
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Update logic to reflect fixes / enhancements added in [email protected]
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+20
-10
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3 files changed

+20
-10
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‎.nf-core.yml

+1
Original file line numberDiff line numberDiff line change
@@ -4,4 +4,5 @@ lint:
44
- assets/email_template.html
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- assets/email_template.txt
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- lib/NfcoreTemplate.groovy
7+
- pyproject.toml
78
multiqc_config: false

‎nextflow_schema.json

+16
Original file line numberDiff line numberDiff line change
@@ -122,6 +122,7 @@
122122
"bbsplit_fasta_list": {
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"type": "string",
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"format": "file-path",
125+
"exists": true,
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"mimetype": "text/plain",
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"fa_icon": "fas fa-list-alt",
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"description": "Path to comma-separated file containing a list of reference genomes to filter reads against with BBSplit. You have to also explicitly set `--skip_bbsplit false` if you want to use BBSplit.",
@@ -130,6 +131,7 @@
130131
"bbsplit_index": {
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"type": "string",
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"format": "path",
134+
"exists": true,
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"fa_icon": "fas fa-bezier-curve",
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"description": "Path to directory or tar.gz archive for pre-built BBSplit index.",
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"help_text": "The BBSplit index will have to be built at least once with this pipeline (see `--save_reference` to save index). It can then be provided via `--bbsplit_index` for future runs."
@@ -154,6 +156,7 @@
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"ribo_database_manifest": {
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"type": "string",
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"format": "file-path",
159+
"exists": true,
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"mimetype": "text/plain",
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"default": "${projectDir}/assets/rrna-db-defaults.txt",
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"fa_icon": "fas fa-database",
@@ -193,6 +196,7 @@
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"gtf": {
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"type": "string",
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"format": "file-path",
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"exists": true,
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"mimetype": "text/plain",
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"pattern": "^\\S+\\.gtf(\\.gz)?$",
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"description": "Path to GTF annotation file.",
@@ -202,6 +206,7 @@
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"gff": {
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"type": "string",
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"format": "file-path",
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"exists": true,
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"mimetype": "text/plain",
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"pattern": "^\\S+\\.gff(\\.gz)?$",
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"fa_icon": "fas fa-code-branch",
@@ -211,6 +216,7 @@
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"gene_bed": {
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"type": "string",
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"format": "file-path",
219+
"exists": true,
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"mimetype": "text/plain",
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"pattern": "^\\S+\\.bed(\\.gz)?$",
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"fa_icon": "fas fa-procedures",
@@ -219,6 +225,7 @@
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"transcript_fasta": {
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"type": "string",
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"format": "file-path",
228+
"exists": true,
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"mimetype": "text/plain",
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"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
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"fa_icon": "far fa-file-code",
@@ -227,6 +234,7 @@
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"additional_fasta": {
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"type": "string",
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"format": "file-path",
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"exists": true,
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"mimetype": "text/plain",
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"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
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"fa_icon": "far fa-file-code",
@@ -236,31 +244,36 @@
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"splicesites": {
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"type": "string",
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"format": "file-path",
247+
"exists": true,
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"mimetype": "text/plain",
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"fa_icon": "fas fa-hand-scissors",
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"description": "Splice sites file required for HISAT2."
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},
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"star_index": {
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"type": "string",
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"format": "path",
255+
"exists": true,
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"fa_icon": "fas fa-bezier-curve",
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"description": "Path to directory or tar.gz archive for pre-built STAR index."
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},
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"hisat2_index": {
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"type": "string",
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"format": "path",
262+
"exists": true,
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"fa_icon": "fas fa-bezier-curve",
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"description": "Path to directory or tar.gz archive for pre-built HISAT2 index."
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},
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"rsem_index": {
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"type": "string",
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"format": "path",
269+
"exists": true,
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"fa_icon": "fas fa-bezier-curve",
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"description": "Path to directory or tar.gz archive for pre-built RSEM index."
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},
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"salmon_index": {
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"type": "string",
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"format": "path",
276+
"exists": true,
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"fa_icon": "fas fa-bezier-curve",
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"description": "Path to directory or tar.gz archive for pre-built Salmon index."
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},
@@ -694,6 +707,7 @@
694707
"multiqc_config": {
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"type": "string",
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"format": "file-path",
710+
"exists": true,
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"mimetype": "text/plain",
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"description": "Custom config file to supply to MultiQC.",
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"fa_icon": "fas fa-cog",
@@ -702,6 +716,7 @@
702716
"multiqc_logo": {
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"type": "string",
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"format": "file-path",
719+
"exists": true,
705720
"mimetype": "text/plain",
706721
"description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
707722
"fa_icon": "fas fa-image",
@@ -710,6 +725,7 @@
710725
"multiqc_methods_description": {
711726
"type": "string",
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"format": "file-path",
728+
"exists": true,
713729
"mimetype": "text/plain",
714730
"description": "Custom MultiQC yaml file containing HTML including a methods description.",
715731
"fa_icon": "fas fa-cog"

‎workflows/rnaseq.nf

+3-10
Original file line numberDiff line numberDiff line change
@@ -193,19 +193,12 @@ workflow RNASEQ {
193193
.fromSamplesheet("input")
194194
.map {
195195
meta, fastq_1, fastq_2 ->
196-
if (!fastq_1.exists()) {
197-
error("Please check input samplesheet -> Read 1 FastQ file does not exist!\n${fastq_1}")
198-
}
199-
if (fastq_2) {
200-
if(!fastq_2.exists()) {
201-
error("Please check input samplesheet -> Read 2 FastQ file does not exist!\n${fastq_2}")
202-
}
203-
return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
204-
} else {
196+
if (!fastq_2) {
205197
return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ]
198+
} else {
199+
return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
206200
}
207201
}
208-
.unique()
209202
.groupTuple()
210203
.map {
211204
WorkflowRnaseq.validateInput(it)

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