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changed the way that ch_sample is generated, shifted to much more simple function from nf-schema, continually making changes based off of linting results, still not working on 26>
1 parent 40bb8ad commit 3e675b2

15 files changed

Lines changed: 69 additions & 74 deletions

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‎conf/test.config‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -81,14 +81,14 @@ params {
8181
skip_sqanti_qc = true
8282
sqanti_qc_reference = 'human'
8383
sqanti_qc_cage = true
84-
sqanti_qc_cage_path = null
84+
sqanti_qc_cage_path = ''
8585
sqanti_qc_polyA_sites = true
86-
sqanti_qc_polyA_sites_path = null
86+
sqanti_qc_polyA_sites_path = ''
8787
sqanti_qc_polyA_motif = true
88-
sqanti_qc_polyA_motif_path = null
88+
sqanti_qc_polyA_motif_path = ''
8989
sqanti_qc_intron_junctions = true
90-
sqanti_qc_intron_path = null
91-
extra_sqanti_qc_options = null
90+
sqanti_qc_intron_path = ''
91+
extra_sqanti_qc_options = ''
9292
help = false
9393
}
9494

‎conf/test_full.config‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -75,13 +75,13 @@ params {
7575
skip_sqanti_qc = true
7676
sqanti_qc_reference = 'human'
7777
sqanti_qc_cage = false
78-
sqanti_qc_cage_path = null
78+
sqanti_qc_cage_path = ''
7979
sqanti_qc_polyA_sites = false
80-
sqanti_qc_polyA_sites_path = null
80+
sqanti_qc_polyA_sites_path = ''
8181
sqanti_qc_polyA_motif = false
82-
sqanti_qc_polyA_motif_path = null
82+
sqanti_qc_polyA_motif_path = ''
8383
sqanti_qc_intron_junctions = false
84-
sqanti_qc_intron_path = null
84+
sqanti_qc_intron_path = ''
8585
extra_sqanti_qc_options = null
8686
help = false
8787
}

‎conf/test_gzipped.config‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -79,14 +79,14 @@ params {
7979
skip_sqanti_qc = true
8080
sqanti_qc_reference = 'human'
8181
sqanti_qc_cage = true
82-
sqanti_qc_cage_path = null
82+
sqanti_qc_cage_path = ''
8383
sqanti_qc_polyA_sites = true
84-
sqanti_qc_polyA_sites_path = null
84+
sqanti_qc_polyA_sites_path = ''
8585
sqanti_qc_polyA_motif = true
86-
sqanti_qc_polyA_motif_path = null
86+
sqanti_qc_polyA_motif_path = ''
8787
sqanti_qc_intron_junctions = true
88-
sqanti_qc_intron_path = null
89-
extra_sqanti_qc_options = null
88+
sqanti_qc_intron_path = ''
89+
extra_sqanti_qc_options = ''
9090
help = false
9191
}
9292

‎main.nf‎

Lines changed: 11 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -16,12 +16,19 @@ nextflow.enable.dsl = 2
1616
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1717
*/
1818

19-
include { DIRECTRNA } from './workflows/directrna'
2019
include { validateParameters } from 'plugin/nf-schema'
2120
include { paramsSummaryLog } from 'plugin/nf-schema'
21+
//include { samplesheetToList } from 'plugin/nf-scheme'
2222
include { paramsHelp } from 'plugin/nf-schema'
23+
include { LONGTX } from './workflows/longtranscriptomics'
2324

24-
workflow{
25+
/*
26+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
27+
RUN MAIN WORKFLOW
28+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
29+
*/
30+
31+
workflow {
2532

2633
main:
2734

@@ -42,19 +49,10 @@ workflow{
4249
exit 0
4350
}
4451

45-
DIRECTRNA()
52+
LONGTX()
4653
}
47-
/*
48-
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
49-
RUN MAIN WORKFLOW
50-
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
51-
*/
52-
/*
53-
workflow {
5454

55-
main:
56-
57-
PIPELINE_COMPLETION (
55+
/* PIPELINE_COMPLETION (
5856
params.email,
5957
params.email_on_fail,
6058
params.plaintext_email,
@@ -63,8 +61,6 @@ workflow {
6361
params.hook_url,
6462
//MEDGEN_DIRECTRNA.out.multiqc_report
6563
)
66-
67-
}
6864
*/
6965

7066
/*

‎modules/local/bedtools/jaccard/main.nf‎

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,6 @@ process BEDTOOLS_JACCARD {
55
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
66
'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_2':
77
'biocontainers/bedtools:2.31.1--hf5e1c6e_2' }"
8-
//publishDir "
98

109
input:
1110
tuple val(meta), path(corrected_bed)
@@ -20,7 +19,7 @@ process BEDTOOLS_JACCARD {
2019
task.ext.when == null || task.ext.when
2120

2221
script:
23-
def args = task.ext.args ?: ''
22+
//def args = task.ext.args ?: ''
2423
def prefix = task.ext.prefix ?: "${meta.id}_${meta.replicate}_${program}"
2524
"""
2625
bedtools \\
@@ -36,7 +35,7 @@ process BEDTOOLS_JACCARD {
3635
"""
3736

3837
stub:
39-
def args = task.ext.args ?: ''
38+
//def args = task.ext.args ?: ''
4039
def prefix = task.ext.prefix ?: "${meta.id}_${meta.replicate}_${program}"
4140
"""
4241
touch ${prefix}.jaccard

‎modules/local/cramino/cramino/main.nf‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -19,13 +19,13 @@ process CRAMINO {
1919

2020
script:
2121
def args = task.ext.args ?: '--spliced'
22-
def read_length = task.ext.read_length ?: "--min-read-len ${read_length}"
22+
def read_len = task.ext.read_length ?: "--min-read-len ${read_length}"
2323
def prefix = task.ext.prefix ?: "${meta.id}_${meta.replicate}_cramino"
2424
"""
2525
cramino \\
2626
-t $task.cpus \\
2727
$args \\
28-
$read_length \\
28+
$read_len \\
2929
$bam \\
3030
> ${prefix}.stats
3131
@@ -36,7 +36,7 @@ process CRAMINO {
3636
"""
3737

3838
stub:
39-
def args = task.ext.args ?: '--spliced'
39+
//def args = task.ext.args ?: '--spliced'
4040
def prefix = task.ext.prefix ?: "${meta.id}"
4141
"""
4242
touch ${prefix}.bam

‎modules/local/curl/curl/main.nf‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
process CURL {
2-
tag "$download"
2+
tag "$prefix"
33
label 'process_single'
44
conda "${moduleDir}/environment.yml"
55
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

‎modules/local/isoquant/isoquant/main.nf‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -61,7 +61,7 @@ process ISOQUANT {
6161
def args = task.ext.args ?: ''
6262
def prefix = task.ext.prefix ?: "${meta.id}_${meta.replicate}_isoquant"
6363
def input_bam = task.ext.input_bam ?: "--bam $bam"
64-
def ref_genome = task.ext.ref_genome ?: "--reference $genome_fasta"
64+
def ref_genome = task.ext.ref_genome ?: "--reference $genome_fasta_index"
6565
def ref_gtf = task.ext.ref_gtf ?: "--genedb $annotation_gtf"
6666
//def output = task.ext.output ?: "--output isoquant_${meta.id}_${meta.replicate}"
6767
//touch ${prefix}.bam

‎modules/local/jaffal/bpipe/main.nf‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
process JAFFAL {
2-
echo true
2+
debug true
33
label 'process_high'
44
conda "bioconda::jaffa=2.3.0"
55
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

‎modules/local/ngsbits/mapping_qc/main.nf‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -20,10 +20,10 @@ process NGS_BITS {
2020
task.ext.when == null || task.ext.when
2121

2222
script:
23-
def args = task.ext.args ?: ''
24-
def contamination = task.ext.contamination ?: "-no_cont"
25-
def genome_build = task.ext.build ?: "$build"
26-
def prefix = task.ext.prefix ?: "${meta.id}_${meta.replicate}_ngsbits"
23+
//def args = task.ext.args ?: ''
24+
def contamination_type = task.ext.contamination ?: "-no_cont"
25+
//def genome_build = task.ext.genome_build ?: "$build"
26+
def prefix = task.ext.prefix ?: "${meta.id}_${meta.replicate}_ngsbits"
2727

2828
// -build $genome_build
2929
"""
@@ -33,7 +33,7 @@ process NGS_BITS {
3333
-rna \\
3434
-ref $genome_fasta \\
3535
-long_read \\
36-
$contamination
36+
$contamination_type
3737
3838
cat <<-END_VERSIONS > versions.yml
3939
"${task.process}":
@@ -42,9 +42,9 @@ process NGS_BITS {
4242
"""
4343

4444
stub:
45-
def args = task.ext.args ?: ''
46-
def contamination = task.ext.contamination ? "-no_cont" : ""
47-
def build = task.ext.build ?: "$build"
45+
//def args = task.ext.args ?: ''
46+
//def contamination = task.ext.contamination ? "-no_cont" : ""
47+
//def build = task.ext.build ?: "$build"
4848
def prefix = task.ext.prefix ?: "${meta.id}_${meta.replicate}_ngsbits"
4949

5050
"""

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