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General refactor and format #142

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5e5d422
formatting
lmReef Apr 17, 2025
451da46
refactor tool config
lmReef Apr 22, 2025
045949b
remove unused params
lmReef Apr 22, 2025
753ced9
use passed vals not params
lmReef Apr 22, 2025
90ade35
fix bitwise or
lmReef Apr 22, 2025
376ad15
remove unused channel
lmReef Apr 22, 2025
0dd469d
formatting
lmReef Apr 22, 2025
078cd38
remove old unused htseq module
lmReef Apr 22, 2025
47f4592
formatting
lmReef Apr 22, 2025
d533807
formatting
lmReef Apr 22, 2025
8360dc3
simplify closures for clarity
lmReef Apr 22, 2025
153c5d4
remove git ignore because lint
lmReef Apr 23, 2025
23be7a6
fix: add ch_reads back in
lmReef Apr 29, 2025
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48 changes: 24 additions & 24 deletions conf/base.config
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Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,13 @@
process {

// TODO nf-core: Check the defaults for all processes
cpus = { 1 * task.attempt }
memory = { 6.GB * task.attempt }
time = { 4.h * task.attempt }
cpus = { 1 * task.attempt }
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I see what you've done here, and I'm fine with it. There is a general approach that people seem to like anf that the template generates that the equals sighs are vertical.

memory = { 6.GB * task.attempt }
time = { 4.h * task.attempt }

errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
maxRetries = 1
maxErrors = '-1'
maxRetries = 1
maxErrors = '-1'

// Process-specific resource requirements
// NOTE - Please try and reuse the labels below as much as possible.
Expand All @@ -26,40 +26,40 @@ process {
// adding in your local modules too.
// TODO nf-core: Customise requirements for specific processes.
// See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
withLabel:process_single {
cpus = { 1 }
withLabel: process_single {
cpus = { 1 }
memory = { 6.GB * task.attempt }
time = { 4.h * task.attempt }
time = { 4.h * task.attempt }
}
withLabel:process_low {
cpus = { 2 * task.attempt }
withLabel: process_low {
cpus = { 2 * task.attempt }
memory = { 12.GB * task.attempt }
time = { 4.h * task.attempt }
time = { 4.h * task.attempt }
}
withLabel:process_medium {
cpus = { 6 * task.attempt }
withLabel: process_medium {
cpus = { 6 * task.attempt }
memory = { 36.GB * task.attempt }
time = { 8.h * task.attempt }
time = { 8.h * task.attempt }
}
withLabel:process_high {
cpus = { 12 * task.attempt }
withLabel: process_high {
cpus = { 12 * task.attempt }
memory = { 72.GB * task.attempt }
time = { 16.h * task.attempt }
time = { 16.h * task.attempt }
}
withLabel:process_long {
time = { 20.h * task.attempt }
withLabel: process_long {
time = { 20.h * task.attempt }
}
withLabel:process_high_memory {
withLabel: process_high_memory {
memory = { 200.GB * task.attempt }
}
withLabel:error_ignore {
withLabel: error_ignore {
errorStrategy = 'ignore'
}
withLabel:error_retry {
withLabel: error_retry {
errorStrategy = 'retry'
maxRetries = 2
maxRetries = 2
}
withName:CUSTOM_DUMPSOFTWAREVERSIONS {
withName: CUSTOM_DUMPSOFTWAREVERSIONS {
cache = false
}
}
816 changes: 408 additions & 408 deletions conf/igenomes.config
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15 changes: 8 additions & 7 deletions conf/modules.config
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Expand Up @@ -78,7 +78,7 @@ process {
// SALMON SA
// -----------------------------

if (params.run_salmon_SA) {
if (params.salmon_sa) {

withName: 'NFCORE_DUALRNASEQ:DUALRNASEQ:SALMON_SELECTIVE_ALIGNMENT:SALMON_INDEX' {
publishDir = [
Expand Down Expand Up @@ -128,12 +128,13 @@ process {
// SALMON AB
// -----------------------------

if (params.run_salmon_AB) {
if (params.salmon_ab) {

withName: 'NFCORE_DUALRNASEQ:DUALRNASEQ:SALMON_ALIGNMENT_BASED:STAR_GENOMEGENERATE' {
ext.args = '--sjdbGTFfeatureExon quant --sjdbGTFtagExonParentTranscript parent'
publishDir = [
path: { "${params.outdir}/salmon_AB/star/" },

mode: params.publish_dir_mode
]
}
Expand Down Expand Up @@ -196,7 +197,7 @@ process {
// STAR GENOME
// -----------------------------

if (params.run_star) {
if (params.star) {

withName: 'NFCORE_DUALRNASEQ:DUALRNASEQ:STAR_ALIGNMENT:STAR_GENOMEGENERATE' {
ext.args = '--sjdbGTFfeatureExon quant --sjdbGTFtagExonParentTranscript parent'
Expand Down Expand Up @@ -230,7 +231,7 @@ process {
// HTSEQ
// -----------------------------

if (params.run_htseq) {
if (params.htseq) {

withName: 'NFCORE_DUALRNASEQ:DUALRNASEQ:PREPARE_REFERENCE_FILES:COMBINE_PATHOGEN_HOST_GFF_FILES_HTSEQ' {
publishDir = [
Expand Down Expand Up @@ -281,7 +282,7 @@ process {
${fastqc_args_value} \
--quiet
""".trim()
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('fastqc')) }
ext.when = { params.fastqc }
publishDir = [
[
path: { "${params.outdir}/fastqc/${meta.id}" },
Expand All @@ -297,7 +298,7 @@ process {
${fastqc_args_value} \
--quiet
""".trim()
ext.when = { !(params.skip_tools && (params.skip_tools.split(',').contains('fastqc') || params.skip_tools.split(',').contains('cutadapt'))) }
ext.when = { params.fastqc && (params.cutadapt) }
publishDir = [
[
path: { "${params.outdir}/fastqc_after_trimming/${meta.id}" },
Expand All @@ -317,7 +318,7 @@ process {
${cutadapt_args_value} \
--quiet
""".trim()
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('cutadapt')) }
ext.when = { params.cutadapt }
publishDir = [
[
path: { "${params.outdir}/cutadapt/${meta.id}" },
Expand Down
8 changes: 4 additions & 4 deletions conf/test.config
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Original file line number Diff line number Diff line change
Expand Up @@ -14,12 +14,12 @@ process {
resourceLimits = [
cpus: 2,
memory: '6.GB',
time: '1.h'
time: '1.h',
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I thought the last item doesn't require a comma?

]
}

params {
config_profile_name = 'Test profile'
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions
Expand All @@ -37,13 +37,13 @@ params {

// Genome references
//genome = 'R64-1-1'
host_fasta_genome = "data/GRCh38.p13_sub.fasta"
host_fasta_genome = "data/GRCh38.p13_sub.fasta"
host_gff = "data/Human_gencode.v33_sub.gff3"

pathogen_fasta_transcripts = "data/SL1344_sub_transcriptome.fasta"
host_fasta_transcripts = "data/Human_gencode.v33_sub_transcriptome.fasta"
libtype = ""

pathogen_fasta_genome = "data/SL1344_sub.fasta"
pathogen_fasta_genome = "data/SL1344_sub.fasta"
pathogen_gff = "data/SL1344_sub.gff3"
}
12 changes: 6 additions & 6 deletions conf/test_2_fasta_pathogen.config
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Original file line number Diff line number Diff line change
Expand Up @@ -5,25 +5,25 @@
Defines input files and everything required to run a fast and simple pipeline test.

Use as follows:
nextflow run nf-core/dualrnaseq -profile test_hackathon,<docker/singularity> --outdir <OUTDIR>
nextflow run nf-core/dualrnaseq -profile test_2_fasta_pathogen,<docker/singularity> --outdir <OUTDIR>
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I agree the naming should be different. This naming doesn't quite make sense as the fasta contains host and pathogen reads.
Perhaps test_small as the files are small and were designed on purpose for fast testing run-times


----------------------------------------------------------------------------------------
*/

params {
config_profile_name = 'Test profile'
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'
max_time = '6.h'

input = "https://raw.githubusercontent.com/nf-core/test-datasets/dualrnaseq/spreadsheet/spreadsheet.csv"
input = "https://raw.githubusercontent.com/nf-core/test-datasets/dualrnaseq/spreadsheet/spreadsheet.csv"

// Genome references

fasta_host = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/GRCh38.p13_sub.fasta"
fasta_host = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/GRCh38.p13_sub.fasta"
gff_host = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/Human_gencode.v33_sub.gff3"
gff_host_tRNA = "data/human.tRNAs.gff.gz"
transcript_fasta_pathogen = "data/SL1344_sub_transcriptome.fasta"
Expand Down
2 changes: 1 addition & 1 deletion conf/test_full.config
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
*/

params {
config_profile_name = 'Full test profile'
config_profile_name = 'Full test profile'
config_profile_description = 'Full test dataset to check pipeline function'

// Input data for full size test
Expand Down
51 changes: 25 additions & 26 deletions conf/test_local.config
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Original file line number Diff line number Diff line change
Expand Up @@ -5,13 +5,13 @@
Defines input files and everything required to run a fast and simple pipeline test.

Use as follows:
nextflow run nf-core/dualrnaseq -profile test_hackathon,<docker/singularity> --outdir <OUTDIR>
nextflow run nf-core/dualrnaseq -profile test_local,<docker/singularity> --outdir <OUTDIR>

----------------------------------------------------------------------------------------
*/

params {
config_profile_name = 'Test profile with small files'
config_profile_name = 'Test profile with small files'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Ignore igenomes
Expand All @@ -26,7 +26,7 @@ params {
// Genome references

// fasta_host = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/GRCh38.p13_sub.fasta"
host_fasta_genome = "data/GRCh38.p13_sub.fasta"
host_fasta_genome = "data/GRCh38.p13_sub.fasta"
host_gff = "data/Human_gencode.v33_sub.gff3"
// gff_host = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/Human_gencode.v33_sub.gff3"
// gff_host_tRNA = 'data/human.tRNAs.gff'
Expand All @@ -36,40 +36,39 @@ params {

// fasta_pathogen = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/SL1344_sub.fasta"
// gff_pathogen = "https://github.com/nf-core/test-datasets/raw/dualrnaseq/references/SL1344_sub.gff3"
pathogen_fasta_genome = "data/SL1344_sub.fasta"
pathogen_fasta_genome = "data/SL1344_sub.fasta"
pathogen_gff = "data/SL1344_sub.gff3"

}

process {
// Override the label definitions so can run locally
withLabel:process_single {
cpus = 1
memory = 2.GB
time = '5m'
// Override the label definitions so can run locally
withLabel: process_single {
cpus = 1
memory = 2.GB
time = '5m'
}

withLabel:process_low {
cpus = 1
memory = 4.GB
time = '5m'
withLabel: process_low {
cpus = 1
memory = 4.GB
time = '5m'
}

withLabel:process_medium {
cpus = 2
memory = 6.GB
time = '5m'
withLabel: process_medium {
cpus = 2
memory = 6.GB
time = '5m'
}

withLabel:process_high {
cpus = 2
memory = 6.GB
time = '5m'
withLabel: process_high {
cpus = 2
memory = 6.GB
time = '5m'
}

withLabel:process_high_memory {
cpus = 2
memory = 6.GB
time = '5m'
withLabel: process_high_memory {
cpus = 2
memory = 6.GB
time = '5m'
}
}
24 changes: 8 additions & 16 deletions main.nf
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Expand Up @@ -16,9 +16,9 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { DUALRNASEQ } from './workflows/dualrnaseq'
include { DUALRNASEQ } from './workflows/dualrnaseq'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_dualrnaseq_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_dualrnaseq_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_dualrnaseq_pipeline'
// include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_dualrnaseq_pipeline'


Expand Down Expand Up @@ -53,7 +53,7 @@ workflow NFCORE_DUALRNASEQ {
//
// WORKFLOW: Run pipeline
//
DUALRNASEQ (samplesheet)
DUALRNASEQ(samplesheet)

emit:
multiqc_report = DUALRNASEQ.out.multiqc_report // channel: /path/to/multiqc_report.html
Expand All @@ -68,42 +68,34 @@ workflow NFCORE_DUALRNASEQ {
*/

workflow {

main:
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION (
PIPELINE_INITIALISATION(
params.version,
params.validate_params,
params.monochrome_logs,
args,
params.outdir,
params.input
params.input,
)

//
// WORKFLOW: Run main workflow
//
NFCORE_DUALRNASEQ (
NFCORE_DUALRNASEQ(
PIPELINE_INITIALISATION.out.samplesheet
)
//
// SUBWORKFLOW: Run completion tasks
//
PIPELINE_COMPLETION (
PIPELINE_COMPLETION(
params.email,
params.email_on_fail,
params.plaintext_email,
params.outdir,
params.monochrome_logs,
params.hook_url,
NFCORE_DUALRNASEQ.out.multiqc_report
NFCORE_DUALRNASEQ.out.multiqc_report,
)
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
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