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number-25number-25
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some more schema tweaking, help etc - still not functioning as expected
1 parent b0aa23a commit 4980e4a

14 files changed

+168
-14
lines changed

‎assets/test_data/KCMF1_hg38.fa.gz‎

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‎assets/test_data/KCMF1_hg38_transcript.fa.gz‎

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‎assets/test_data/KCMF1_hg38_transcript.gtf.gz‎

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‎assets/test_data/chr22_1-17500000.fa.gz‎

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‎assets/test_data/chr22_1-17500000.gtf.gz‎

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‎assets/test_data/dummy_sequencing_summary.txt‎

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‎conf/test.config‎

Lines changed: 10 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -82,7 +82,16 @@ params {
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sqanti_qc_intron_junctions = true
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sqanti_qc_intron_path = null
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extra_sqanti_qc_options = null
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help = false
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help = true
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}
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validation {
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help {
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enabled = true
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beforeText = "Welcome to LongTranscriptomics, I see you are seeking help."
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afterText = "Farewell, hopefully this was helpful. Please cite the pipeline owners when using this pipeline."
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command = "nextflow run . -profile <profile> --outdir <outdir>"
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}
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}
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includeConfig "../modules/local/isoquant/isoquant/test_nextflow.config"

‎conf/test_full.config‎

Lines changed: 13 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -28,13 +28,13 @@ params {
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bam_input = false
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// Genome references
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// These channel names have to match those in the full workflow also
31-
genome_fasta = "assets/fulltest_data/hg38.analysisSet.fa"
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genome_fasta = "assets/fulltest_data/hg38.analysisSet.fa.gz"
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genome_fasta_index = "assets/fulltest_data/hg38.analysisSet.fa.fai"
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genome_fasta_sizes = null
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genome_minimap2_index = null
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transcriptome_fasta = "assets/fulltest_data/Homo_sapiens.GRCh38.112_chr_transcripts.fa"
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transcriptome_fasta = "assets/fulltest_data/Homo_sapiens.GRCh38.112_chr_transcripts.fa.gz"
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transcriptome_minimap2_index = null
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annotation_gtf = "assets/fulltest_data/Homo_sapiens.GRCh38.112_chr.gtf"
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annotation_gtf = "assets/fulltest_data/Homo_sapiens.GRCh38.112_chr.gtf.gz"
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skip_prepare_reference = false
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skip_mapping = false
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skip_bam_to_bigwig = false
@@ -81,5 +81,14 @@ params {
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sqanti_qc_intron_junctions = false
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sqanti_qc_intron_path = null
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extra_sqanti_qc_options = null
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help = false
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help = true
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}
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validation {
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help {
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enabled = true
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beforeText = "Welcome to LongTranscriptomics, I see you are seeking help."
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afterText = "Farewell, hopefully this was helpful. "Please cite the pipeline owners when using this pipeline."
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command = "nextflow run . -profile <profile> --outdir <outdir>"
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}
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}

‎conf/test_gzipped.config‎

Lines changed: 129 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,129 @@
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a fast and simple pipeline test.
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Use as follows:
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nextflow run . -profile test,<docker/singularity> --outdir <OUTDIR>
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----------------------------------------------------------------------------------------
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*/
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params {
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config_profile_name = 'Test profile'
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config_profile_description = 'Minimal test dataset to check pipeline function'
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config_profile_url = "https://github.com/number-25/LongTranscriptomics/blob/dev/conf/test.config"
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// Limit resources so that this can run on GitHub Actions
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max_cpus = 2
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max_memory = '6.GB'
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max_time = '12.h'
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// Input data
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input = 'test/samplesheets/samplesheet_test_dRNA.csv'
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sequencing_type = "ont-drna" // sequencing molecule [ont-drna OR ont-cdna]
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bam_input = false
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// Genome references
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// These channel names have to match those in the full workflow also
29+
genome_fasta = "assets/test_data/KCMF1_hg38.fa"
30+
genome_fasta_index = "assets/test_data/KCMF1_hg38.fa.fai"
31+
genome_fasta_sizes = "assets/test_data/KCMF1_hg38.fa.sizes"
32+
genome_minimap2_index = "assets/test_data/KCMF1_hg38_k14.mmi"
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transcriptome_fasta = "assets/test_data/KCMF1_hg38_transcript.fa"
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transcriptome_minimap2_index = "assets/test_data/KCMF1_hg38_transcript_k14.mmi"
35+
annotation_gtf = "assets/test_data/KCMF1_hg38_transcript.gtf"
36+
skip_prepare_reference = true
37+
//annotation_gtf = "https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/reference/chr22_1-17500000.gtf"
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//genome_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/reference/chr22_1-17550000.fa'
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//input_path = 'https://github.com/nf-core/test-datasets/blob/nanoseq/fastq/demultiplexed/quantification/bambu/MCF7_directRNA_replicate4.fastq.gz'
40+
// Skip processes for test
41+
// Give any required params for the test so that command line flags are not needed
42+
skip_mapping = false
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skip_bam_to_bigwig = false
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skip_qc = false
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skip_bam_qc = false
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skip_nanoq = false
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skip_sequali = false
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skip_alfred = false
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skip_cramino = false
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skip_samtools_flagstat = false
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skip_ngs_bits = true
52+
ngs_bits_skip_contamination = true // default: [false]
53+
ngs_bits_build = 'hg38' // options: [hg38, hg19, non_human]
54+
cramino_min_length = 0 // minimum re
55+
skip_jaccard = true
56+
skip_flair = true
57+
skip_flair_correct = true
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skip_flair_collapse = true
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extra_flair_collapse_options = null
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skip_bambu = true
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skip_isoquant = true
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skip_isoquant_correction = true
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extra_isoquant_options = null
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skip_stringtie = false
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extra_stringtie_options = null
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skip_jaffal = true
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skip_jaffal_download = true
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// TRANSCRIPT QUANTIFICATION
69+
skip_transcript_quantification = false
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skip_oarfish = false
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skip_sqanti_all = true
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skip_gffcompare = false
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extra_gffcompare_options = null
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skip_sqanti_qc = true
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sqanti_qc_reference = 'human'
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sqanti_qc_cage = true
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sqanti_qc_cage_path = null
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sqanti_qc_polyA_sites = true
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sqanti_qc_polyA_sites_path = null
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sqanti_qc_polyA_motif = true
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sqanti_qc_polyA_motif_path = null
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sqanti_qc_intron_junctions = true
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sqanti_qc_intron_path = null
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extra_sqanti_qc_options = null
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help = true
86+
}
87+
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validation {
89+
help {
90+
enabled = true
91+
beforeText = "Welcome to LongTranscriptomics, I see you are seeking help."
92+
afterText = "Farewell, hopefully this was helpful. Please cite the pipeline owners when using this pipeline."
93+
command = "nextflow run . -profile <profile> --outdir <outdir>"
94+
}
95+
}
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97+
includeConfig "../modules/local/isoquant/isoquant/test_nextflow.config"
98+
includeConfig "../modules/local/gffcompare/gffcompare/nextflow.config"
99+
includeConfig "../modules/local/nanoq/nanoq/nextflow.config"
100+
includeConfig "../modules/local/sequali/sequali/nextflow.config"
101+
includeConfig "../modules/local/minimap2/align/nextflow.config"
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includeConfig "../modules/local/samtools/sort/nextflow.config"
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includeConfig "../modules/local/samtools/index/nextflow.config"
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includeConfig "../modules/local/bedtools/bam_to_bedgraph/nextflow.config"
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includeConfig "../modules/local/bedtools/bam_to_bedgraph/nextflow.config"
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includeConfig "../modules/local/ucsc/bedgraphtobigwig/nextflow.config"
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includeConfig "../modules/local/ucsc/bedclip/nextflow.config"
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includeConfig "../modules/local/alfred/qc/nextflow.config"
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includeConfig "../modules/local/alfred/transpose/nextflow.config"
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includeConfig "../modules/local/cramino/cramino/nextflow.config"
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includeConfig "../modules/local/ngsbits/mapping_qc/nextflow.config"
112+
includeConfig "../modules/local/samtools/flagstat/nextflow.config"
113+
includeConfig "../modules/local/flair/bam_to_bed12/nextflow.config"
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includeConfig "../modules/local/flair/correct/nextflow.config"
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includeConfig "../modules/local/flair/collapse/nextflow.config"
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includeConfig "../modules/local/bambu/bambu/nextflow.config"
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includeConfig "../modules/local/isoquant/isoquant/nextflow.config"
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includeConfig "../modules/local/stringtie/stringtie/nextflow.config"
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includeConfig "../modules/local/gffread/gffread/nextflow.config"
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includeConfig "../modules/local/jaffal/bpipe/nextflow.config"
121+
includeConfig "../modules/local/oarfish/raw_read/nextflow.config"
122+
includeConfig "../modules/local/bedtools/jaccard/nextflow.config"
123+
includeConfig "../modules/local/gffcompare/gffcompare/nextflow.config"
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includeConfig "../modules/local/curl/curl/nextflow.config"
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includeConfig "../modules/local/minimap2/index/nextflow.config"
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includeConfig "../modules/local/unzip/unzip/nextflow.config"
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includeConfig "../modules/nf-core/gunzip/nextflow.config"
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includeConfig "../modules/nf-core/custom/getchromsizes/nextflow.config"
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includeConfig "../modules/local/isoquant/gtf2db/nextflow.config"

‎main.nf‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -19,25 +19,26 @@ nextflow.enable.dsl = 2
1919
include { DIRECTRNA } from './workflows/directrna'
2020
include { validateParameters } from 'plugin/nf-schema'
2121
include { paramsSummaryLog } from 'plugin/nf-schema'
22+
include { paramsHelp } from 'plugin/nf-schema'
2223

2324
workflow{
2425

2526
//
2627
// nf-scheme validations
2728
//
2829

29-
validateParameters()
30+
// validateParameters()
3031
log.info paramsSummaryLog(workflow)
3132

32-
if (params.help) {
33+
/* if (params.help) {
3334
log.info paramsHelp(
3435
beforeText: "Welcome to LongTranscriptomics, I see you are seeking help.",
3536
afterText: "Farewell, hopefully this was helpful.",
3637
command: "nextflow run . -profile <profile> --outdir <outdir>",
3738
)
3839
exit 0
3940
}
40-
41+
*/
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4243
DIRECTRNA ()
4344
}

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