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Lines changed: 40 additions & 52 deletions

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‎conf/test_full.config‎

Lines changed: 16 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -17,16 +17,9 @@ params {
1717
config_profile_description = 'Full test dataset to check pipeline function'
1818

1919
// Input data for full size test
20-
// nf-core: Give any required params for the test so that command line flags are not needed
21-
//input = /test/samplesheets/samplesheet_testfull_dRNA.csv'
2220
//input_path =
2321
//'https://github.com/nf-core/test-datasets/blob/nanoseq/fastq/demultiplexed/quantification/bambu/MCF7_directRNA_replicate4.fastq.gz'
2422

25-
// Limit resources so that this can run on GitHub Actions
26-
//max_cpus = 2
27-
//max_memory = '12.GB'
28-
//max_time = '36.h'
29-
3023
// Input data
3124
//input = 'test/samplesheets/samplesheet_test_dRNA.csv'
3225
input = "test/samplesheets/samplesheet_test_local.csv"
@@ -42,11 +35,6 @@ params {
4235
transcriptome_minimap2_index = null
4336
annotation_gtf = "assets/fulltest_data/Homo_sapiens.GRCh38.112_chr.gtf"
4437
skip_prepare_reference = false
45-
//annotation_gtf = "https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/reference/chr22_1-17500000.gtf"
46-
//genome_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/reference/chr22_1-17550000.fa'
47-
//input_path = 'https://github.com/nf-core/test-datasets/blob/nanoseq/fastq/demultiplexed/quantification/bambu/MCF7_directRNA_replicate4.fastq.gz'
48-
// Skip processes for test
49-
// Give any required params for the test so that command line flags are not needed
5038
skip_mapping = false
5139
skip_bam_to_bigwig = false
5240
skip_qc = false
@@ -57,9 +45,9 @@ params {
5745
skip_cramino = false
5846
skip_samtools_flagstat = false
5947
skip_ngs_bits = false
60-
ngs_bits_skip_contamination = false // default: [false]
48+
ngs_bits_skip_contamination = false // default: [false]
6149
ngs_bits_build = 'hg38' // options: [hg38, hg19, non_human]
62-
cramino_min_length = 0 // minimum required
50+
cramino_min_length = 0 // minimum required
6351
skip_jaccard = false
6452
skip_flair = false
6553
skip_flair_correct = false
@@ -73,24 +61,24 @@ params {
7361
extra_stringtie_options = null
7462
skip_jaffal = true
7563
skip_jaffal_download = true
76-
//jaffal_reference = 'data/jaffal_reference'
77-
jaffal_reference = 'data/for_jaffal'
64+
jaffal_reference = null
7865
// TRANSCRIPT QUANTIFICATION
7966
skip_transcript_quantification = false
8067
skip_oarfish = false
8168
skip_transigner = false
69+
// TRANSCRIPTOME ASSESSMENT
8270
skip_gffcompare = false
8371
extra_gffcompare_options = null
84-
// skip_sqanti_all = true
85-
// skip_sqanti_qc = true
86-
// sqanti_qc_reference = 'human'
87-
// sqanti_qc_cage = false
88-
// sqanti_qc_cage_path = null
89-
// sqanti_qc_polyA_sites = false
90-
// sqanti_qc_polyA_sites_path = null
91-
// sqanti_qc_polyA_motif = false
92-
// sqanti_qc_polyA_motif_path = null
93-
// sqanti_qc_intron_junctions = false
94-
// sqanti_qc_intron_path = null
95-
// extra_sqanti_qc_options = null
72+
skip_sqanti_all = true
73+
skip_sqanti_qc = true
74+
sqanti_qc_reference = 'human'
75+
sqanti_qc_cage = false
76+
sqanti_qc_cage_path = null
77+
sqanti_qc_polyA_sites = false
78+
sqanti_qc_polyA_sites_path = null
79+
sqanti_qc_polyA_motif = false
80+
sqanti_qc_polyA_motif_path = null
81+
sqanti_qc_intron_junctions = false
82+
sqanti_qc_intron_path = null
83+
extra_sqanti_qc_options = null
9684
}

‎modules/local/bambu/bambu/main.nf‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,7 @@ process BAMBU {
55
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
66
'https://depot.galaxyproject.org/singularity/bioconductor-bambu:3.0.8--r42hc247a5b_0' :
77
'docker://quay.io/biocontainers/bioconductor-bambu:3.0.8--r42hc247a5b_0' }"
8+
//containerOptions = '-u $(id -u):$(id -g)'
89
//'number25/bambu:3.8.0':
910
//'docker://quay.io/number_25/bambu:latest' }"
1011
// 'https://depot.galaxyproject.org/singularity/bioconductor-bambu:3.4.0--r43hf17093f_1' :

‎modules/nf-core/gunzip/main.nf‎

Lines changed: 3 additions & 4 deletions
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‎nextflow.config‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -90,13 +90,13 @@ params {
9090
skip_sqanti_qc = false
9191
sqanti_qc_reference = 'human'
9292
sqanti_qc_cage = true
93-
sqanti_qc_cage_path = '/path/to/cage'
93+
sqanti_qc_cage_path = null // path to cage data
9494
sqanti_qc_polyA_sites = true
95-
sqanti_qc_polyA_sites_path = 'path/to/polyA'
95+
sqanti_qc_polyA_sites_path = null // path to polyA sites data
9696
sqanti_qc_polyA_motif = true
97-
sqanti_qc_polyA_motif_path = 'path/to/polyA/path'
97+
sqanti_qc_polyA_motif_path = null // path to polyA motif data
9898
sqanti_qc_intron_junctions = true
99-
sqanti_qc_intron_path = 'path/to/intro/path'
99+
sqanti_qc_intron_path = null // path to intron junction data
100100
extra_sqanti_qc_options = null
101101
// skip_sqanti_filter = false
102102
// extra_sqanti_filter_options = null
@@ -130,15 +130,15 @@ params {
130130
config_profile_description = null
131131
custom_config_version = 'dev'
132132
//custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
133-
custom_config_base = 'https://raw.githubusercontent.com/nf-core/configs/dev'
133+
//custom_config_base = 'https://raw.githubusercontent.com/nf-core/configs/dev'
134134
config_profile_contact = 'deancombio@pm.me'
135135
config_profile_url = ''
136136

137137
// Max resource options
138138
// Defaults only, expecting to be overwritten
139-
//max_memory = '32.GB'
140-
//max_cpus = 10
141-
//max_time = '48.h'
139+
max_memory = '32.GB'
140+
max_cpus = 10
141+
max_time = '48.h'
142142

143143
// Schema validation default options
144144
//validationFailUnrecognisedParams = false

‎subworkflows/local/prepare_reference/main.nf‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -160,7 +160,7 @@ workflow PREPARE_REFERENCE{
160160
ch_sqanti_qc_polyA_sites_bed = SQANTI_PREPARE_REFERENCE.out.sqanti_qc_polyA_sites_bed
161161
ch_sqanti_qc_polyA_motif = SQANTI_PREPARE_REFERENCE.out.sqanti_qc_polyA_motif
162162
ch_sqanti_qc_intron_junctions_bed = SQANTI_PREPARE_REFERENCE.out.sqanti_qc_intron_junctions_bed
163-
ch_versions = ch.versions.mix(SQANTI_PREPARE_REFERENCE.out.versions)
163+
164164
} else {
165165
ch_sqanti_qc_cage_bed = null
166166
ch_sqanti_qc_polyA_sites_bed = null

‎subworkflows/local/sqanti/sqanti_prepare_reference/main.nf‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -35,15 +35,15 @@ workflow SQANTI_PREPARE_REFERENCE {
3535
CURL_CAGE( 'refTSS_CAGE', 'bed.gz', 'https://figshare.com/ndownloader/files/52801133' )
3636
sqanti_cage_bed_gzip = CURL_CAGE.out.curl
3737
ch_versions = ch_versions.mix(CURL_CAGE.out.versions)
38-
ch_sqanti_cage_bed = GUNZIP_CAGE( [ [:], sqanti_cage_bed_gzip ] ).gunzip.map { it[1] }
38+
ch_sqanti_qc_cage_bed = GUNZIP_CAGE( [ [:], sqanti_cage_bed_gzip ] ).gunzip.map { it[1] }
3939
ch_versions = ch_versions.mix(GUNZIP_CAGE.out.versions)
4040
//ch_sqanti_cage_bed = GUNZIP_CAGE.out.
4141
} else {
4242
if (sqanti_qc_cage_path.endsWith('.gz')) {
43-
ch_sqanti_cage_bed = GUNZIP_CAGE( [ [:], sqanti_qc_cage_path ] ).gunzip.map { it[1] }
43+
ch_sqanti_qc_cage_bed = GUNZIP_CAGE( [ [:], sqanti_qc_cage_path ] ).gunzip.map { it[1] }
4444
ch_versions = ch_versions.mix(GUNZIP_CAGE.out.versions)
4545
} else {
46-
ch_sqanti_cage_bed = Channe.value(file(sqanti_qc_cage_path), checkIfExists:true)
46+
ch_sqanti_qc_cage_bed = Channel.value(file(sqanti_qc_cage_path), checkIfExists:true)
4747
}
4848
}
4949
}
@@ -53,7 +53,7 @@ workflow SQANTI_PREPARE_REFERENCE {
5353
CURL_POLYA_SITES( 'polyA_sites', 'bed.gz', 'https://figshare.com/ndownloader/files/52801130' )
5454
sqanti_polyA_sites_bed_gzip = CURL_POLYA_SITES.out.curl
5555
ch_versions = ch_versions.mix(CURL_POLYA_SITES.out.versions)
56-
ch_sqanti_polyA_sites_bed = GUNZIP_POLYA_SITES( [ [:], sqanti_polyA_sites_bed_gzip ] ).gunzip.map { it[1] }
56+
ch_sqanti_qc_polyA_sites_bed = GUNZIP_POLYA_SITES( [ [:], sqanti_polyA_sites_bed_gzip ] ).gunzip.map { it[1] }
5757
ch_versions = ch_versions.mix(GUNZIP_POLYA_SITES.out.versions)
5858
} else {
5959
if (sqanti_polyA_sites_path.endsWith('.gz')) {
@@ -70,9 +70,9 @@ workflow SQANTI_PREPARE_REFERENCE {
7070
if (sqanti_qc_polyA_motif_path == null) { // user doesn't provide path to predownload polyA sites data
7171
CURL_POLYA_MOTIF( 'polyA_motif', 'txt', 'https://figshare.com/ndownloader/files/52801139' )
7272
ch_versions = ch_versions.mix(CURL_POLYA_MOTIF.out.versions)
73-
ch_sqanti_polyA_motif = CURL_POLYA_MOTIF.out.curl
73+
ch_sqanti_qc_polyA_motif = CURL_POLYA_MOTIF.out.curl
7474
} else {
75-
ch_sqanti_polyA_motif = Channel.value(file(sqanti_qc_polyA_motif_path), checkIfExists:true)
75+
ch_sqanti_qc_polyA_motif = Channel.value(file(sqanti_qc_polyA_motif_path), checkIfExists:true)
7676
}
7777
}
7878

@@ -82,22 +82,22 @@ workflow SQANTI_PREPARE_REFERENCE {
8282
CURL_INTROPOLIS( 'intropolis', 'bed.gz', 'https://figshare.com/ndownloader/files/52801127' )
8383
sqanti_intron_junctions_bed_gzip = CURL_INTROPOLIS.out.curl
8484
ch_versions = ch_versions.mix(CURL_INTROPOLIS.out.versions)
85-
ch_sqanti_intron_junctions_bed = GUNZIP_INTROPOLIS( [ [:], sqanti_intron_junctions_bed_gzip ] ).gunzip.map { it[1] }
85+
ch_sqanti_qc_intron_junctions_bed = GUNZIP_INTROPOLIS( [ [:], sqanti_intron_junctions_bed_gzip ] ).gunzip.map { it[1] }
8686
} else {
8787
if (sqanti_qc_intron_path.endsWith('.gz')) {
8888
ch_sqanti_qc_intron_junctions_bed = GUNZIP_INTROPOLIS( [ [:], sqanti_qc_intron_path ] ).gunzip.map { it[1] }
8989
ch_versions = ch_versions.mix(GUNZIP_INTROPOLIS.out.versions)
9090
} else {
91-
ch_sqanti_qc_intron_bed = Channel.value(file(sqanti_qc_intron_path), checkIfExists:true)
91+
ch_sqanti_qc_intron_junctions_bed = Channel.value(file(sqanti_qc_intron_path), checkIfExists:true)
9292
}
9393
}
9494
}
9595
}
9696

9797

9898
emit:
99-
sqanti_qc_cage_bed = ch_sqanti_cage_bed
100-
sqanti_qc_polyA_sites_bed = ch_sqanti_polyA_sites_bed
99+
sqanti_qc_cage_bed = ch_sqanti_qc_cage_bed
100+
sqanti_qc_polyA_sites_bed = ch_sqanti_qc_polyA_sites_bed
101101
sqanti_qc_polyA_motif = ch_sqanti_qc_polyA_motif
102102
sqanti_qc_intron_junctions_bed = ch_sqanti_qc_intron_junctions_bed
103103
versions = ch_versions // channel: [ versions.yml ]

‎workflows/directrna.nf‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -465,7 +465,7 @@ workflow DIRECTRNA{
465465

466466
// Oarfish
467467
// if (!params.skip_quantification && !params.skip_mapping && params.!skip_oarfish)
468-
if (!params.skip_quantification) {
468+
if (!params.skip_transcript_quantification) {
469469
if (!params.skip_oarfish) {
470470
if (!params.skip_flair) {
471471
OARFISH_FLAIR( ch_flair_collapsed_fa, ch_transcriptome_minimap2_index, ch_sequencing_type, 'flair' )

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