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GallVpGallVp
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Fixed snapshots
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‎CHANGELOG.md

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Original file line numberDiff line numberDiff line change
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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1. Gene models from BRAKER with invalid ORF(s) are now removed [#151](https://github.com/Plant-Food-Research-Open/genepal/issues/151)
1111
2. Demoted nf-schema to 2.2.0 to avoid errors with latest Nextflow versions
12+
3. Fixed a nextflow syntax issue in `conf/modules.config`
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### `Dependencies`
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‎conf/modules.config

Lines changed: 62 additions & 66 deletions
Original file line numberDiff line numberDiff line change
@@ -68,78 +68,73 @@ process { // SUBWORKFLOW: PREPARE_ASSEMBLY
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}
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7070
process { // SUBWORKFLOW: PREPROCESS_RNASEQ
71-
if(!params.fastqc_skip) {
72-
withName: '.*:PREPROCESS_RNASEQ:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
73-
ext.args = '--quiet'
7471

75-
publishDir = [
76-
path: { "${params.outdir}/fastqc_raw" },
72+
withName: '.*:PREPROCESS_RNASEQ:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
73+
ext.args = '--quiet'
74+
75+
publishDir = [
76+
path: { "${params.outdir}/fastqc_raw" },
77+
mode: params.publish_dir_mode,
78+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
79+
]
80+
}
81+
82+
withName: '.*:PREPROCESS_RNASEQ:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
83+
ext.args = '--quiet'
84+
ext.prefix = { "${meta.id}_trim" }
85+
publishDir = [
86+
path: { "${params.outdir}/fastqc_trim" },
87+
mode: params.publish_dir_mode,
88+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
89+
]
90+
}
91+
92+
withName: '.*:PREPROCESS_RNASEQ:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' {
93+
ext.args = params.fastp_extra_args ?: ''
94+
publishDir = [
95+
[
96+
path: { "${params.outdir}/fastp/html" },
7797
mode: params.publish_dir_mode,
78-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
98+
pattern: "*.{html}"
99+
],
100+
[
101+
path: { "${params.outdir}/fastp/json" },
102+
mode: params.publish_dir_mode,
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pattern: "*.{json}"
104+
],
105+
[
106+
path: { "${params.outdir}/fastp/log" },
107+
mode: params.publish_dir_mode,
108+
pattern: "*.log"
109+
],
110+
[
111+
path: { "${params.outdir}/fastp" },
112+
mode: params.publish_dir_mode,
113+
pattern: "*.fastq.gz",
114+
enabled: params.save_trimmed
79115
]
80-
}
116+
]
117+
}
118+
119+
withName: '.*:PREPROCESS_RNASEQ:SORTMERNA_INDEX' {
120+
ext.args = '--index 1'
121+
}
81122

82-
withName: '.*:PREPROCESS_RNASEQ:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
83-
ext.args = '--quiet'
84-
ext.prefix = { "${meta.id}_trim" }
85-
publishDir = [
86-
path: { "${params.outdir}/fastqc_trim" },
123+
withName: '.*:PREPROCESS_RNASEQ:SORTMERNA_READS' {
124+
ext.args = '--index 0 --num_alignments 1 -v'
125+
publishDir = [
126+
[
127+
path: { "${params.outdir}/sortmerna" },
87128
mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
89-
]
90-
}
91-
}
92-
93-
if(!params.fastp_skip) {
94-
withName: '.*:PREPROCESS_RNASEQ:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' {
95-
ext.args = params.fastp_extra_args ?: ''
96-
publishDir = [
97-
[
98-
path: { "${params.outdir}/fastp/html" },
99-
mode: params.publish_dir_mode,
100-
pattern: "*.{html}"
101-
],
102-
[
103-
path: { "${params.outdir}/fastp/json" },
104-
mode: params.publish_dir_mode,
105-
pattern: "*.{json}"
106-
],
107-
[
108-
path: { "${params.outdir}/fastp/log" },
109-
mode: params.publish_dir_mode,
110-
pattern: "*.log"
111-
],
112-
[
113-
path: { "${params.outdir}/fastp" },
114-
mode: params.publish_dir_mode,
115-
pattern: "*.fastq.gz",
116-
enabled: params.save_trimmed
117-
]
118-
]
119-
}
120-
}
121-
122-
if (params.remove_ribo_rna) {
123-
withName: '.*:PREPROCESS_RNASEQ:SORTMERNA_INDEX' {
124-
ext.args = '--index 1'
125-
}
126-
127-
withName: '.*:PREPROCESS_RNASEQ:SORTMERNA_READS' {
128-
ext.args = '--index 0 --num_alignments 1 -v'
129-
publishDir = [
130-
[
131-
path: { "${params.outdir}/sortmerna" },
132-
mode: params.publish_dir_mode,
133-
pattern: "*.log"
134-
],
135-
[
136-
path: { "${params.outdir}/sortmerna" },
137-
mode: params.publish_dir_mode,
138-
pattern: "*.fastq.gz",
139-
enabled: params.save_non_ribo_reads
140-
]
129+
pattern: "*.log"
130+
],
131+
[
132+
path: { "${params.outdir}/sortmerna" },
133+
mode: params.publish_dir_mode,
134+
pattern: "*.fastq.gz",
135+
enabled: params.save_non_ribo_reads
141136
]
142-
}
137+
]
143138
}
144139
}
145140

@@ -187,6 +182,7 @@ process { // SUBWORKFLOW: FASTA_BRAKER3
187182
}
188183

189184
withName: '.*:FASTA_BRAKER3:FILTER_INVALID_ORFS' {
185+
ext.prefix = { "${meta.id}.invalid.orf.purged" }
190186
ext.args = '-J --keep-genes'
191187
}
192188
}

‎main.nf

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Original file line numberDiff line numberDiff line change
@@ -30,7 +30,6 @@ workflow PLANTFOODRESEARCHOPEN_GENEPAL {
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3131
take:
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ch_target_assembly
33-
ch_tar_assm_str
3433
ch_is_masked
3534
ch_te_library
3635
ch_braker_annotation
@@ -52,7 +51,6 @@ workflow PLANTFOODRESEARCHOPEN_GENEPAL {
5251
//
5352
GENEPAL(
5453
ch_target_assembly,
55-
ch_tar_assm_str,
5654
ch_is_masked,
5755
ch_te_library,
5856
ch_braker_annotation,
@@ -99,7 +97,6 @@ workflow {
9997
//
10098
PLANTFOODRESEARCHOPEN_GENEPAL(
10199
PIPELINE_INITIALISATION.out.target_assembly,
102-
PIPELINE_INITIALISATION.out.tar_assm_str,
103100
PIPELINE_INITIALISATION.out.is_masked,
104101
PIPELINE_INITIALISATION.out.te_library,
105102
PIPELINE_INITIALISATION.out.braker_annotation,

‎subworkflows/local/fasta_braker3.nf

Lines changed: 3 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -5,8 +5,8 @@ include { GFFREAD as FILTER_INVALID_ORFS } from '../../modules/nf-core/gf
55

66
workflow FASTA_BRAKER3 {
77
take:
8-
ch_masked_target_assembly // channel: [ meta, fasta ]; meta ~ [ id: traget_assembly ]
9-
ch_braker_ex_asm_str // channel: val(assembly_x,assembly_y)
8+
ch_valid_target_assembly // channel: [ meta, fasta ]; meta ~ [ id: target_assembly ]; All input assemblies
9+
ch_masked_target_assembly // channel: [ meta, fasta ]; Assemblies that don't have BRAKER annotations in the input sheet
1010
ch_rnaseq_bam // channel: [ meta, bam ]
1111
ch_ext_prots_fasta // channel: [ meta2, fasta ]; meta2 ~ [ id: ext_protein_seqs ]
1212
ch_braker_annotation // channel: [ meta, gff3, hints.gff ]
@@ -16,11 +16,6 @@ workflow FASTA_BRAKER3 {
1616

1717

1818
ch_braker_inputs = ch_masked_target_assembly
19-
| combine( ch_braker_ex_asm_str )
20-
| filter { meta, fasta, ex_str -> !( ex_str.split(",").contains( meta.id ) ) }
21-
| map { meta, fasta, ex_str ->
22-
[ meta, fasta ]
23-
}
2419
| join(ch_rnaseq_bam, remainder: true)
2520
| combine(
2621
ch_ext_prots_fasta.map { meta, fasta -> fasta }.ifEmpty(null)
@@ -62,7 +57,7 @@ workflow FASTA_BRAKER3 {
6257

6358
// MODULE: GFFREAD as FILTER_INVALID_ORFS
6459
ch_filter_inputs = ch_braker_gff3
65-
| join(ch_masked_target_assembly)
60+
| join(ch_valid_target_assembly)
6661
| multiMap { meta, gff3, fasta ->
6762
gff: [ meta, gff3 ]
6863
fasta: fasta

‎subworkflows/local/preprocess_rnaseq.nf

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,8 +6,7 @@ include { FASTQ_FASTQC_UMITOOLS_FASTP } from '../../subworkflows/nf-core/fastq
66
workflow PREPROCESS_RNASEQ {
77
take:
88
ch_reads // channel: [ [ id, single_end, target_assemblies ], [ [ fq ] ] ]
9-
permissible_assemblies // val: assembly_a,assembly_b
10-
exclude_assemblies // channel: val(assembly_x,assembly_y)
9+
exclude_assemblies // channel: val(assembly_x,assembly_y); To exclude samples for which all assemblies have BRAKER annotations in the input sheet
1110
fastqc_skip // val: true|false
1211
fastp_skip // val: true|false
1312
save_trimmed // val: true|false

‎subworkflows/local/utils_nfcore_genepal_pipeline/main.nf

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Original file line numberDiff line numberDiff line change
@@ -297,7 +297,6 @@ workflow PIPELINE_INITIALISATION {
297297

298298
emit:
299299
target_assembly = ch_target_assembly
300-
tar_assm_str = ch_tar_assm_str
301300
is_masked = ch_is_masked
302301
te_library = ch_te_library
303302
braker_annotation = ch_braker_annotation

‎tests/minimal/main.nf.test.snap

Lines changed: 19 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
"profile - test": {
33
"content": [
44
{
5-
"successful tasks": 21,
5+
"successful tasks": 22,
66
"versions": {
77
"AGAT_CONVERTSPGFF2GTF": {
88
"agat": "v1.4.1"
@@ -40,6 +40,9 @@
4040
"FILTER_BY_ORF_SIZE": {
4141
"agat": "v1.4.3"
4242
},
43+
"FILTER_INVALID_ORFS": {
44+
"gffread": "0.12.7"
45+
},
4346
"FINAL_GFF_CHECK": {
4447
"genometools": "1.6.5"
4548
},
@@ -68,12 +71,12 @@
6871
}
6972
},
7073
"stable paths": [
71-
"a_thaliana.cdna.fasta:md5,f44a6acdc245b85a935ef9ed3fc62967",
72-
"a_thaliana.cds.fasta:md5,4fd5a251a3912b452844e1f7332f514d",
73-
"a_thaliana.gt.gff3:md5,00b2ee481731e9ada62575ebe5eff1e4",
74-
"a_thaliana.pep.fasta:md5,38ae660abc78eb57d467bb48b5170f19",
75-
"a_thaliana.gff3:md5,bc520744a70fd9bf1b4bd4271bc83fc4",
76-
"summary_stats.json:md5,007ba5cf2b7a2fd395a27d9458ca2d2e"
74+
"a_thaliana.cdna.fasta:md5,38e7d3fa40ba9ebf2c7d692fb7100c7c",
75+
"a_thaliana.cds.fasta:md5,740b56d0df4a8f89b8eafd62242c8672",
76+
"a_thaliana.gt.gff3:md5,b774df188a0db9eb9b8c2c60fa3e627a",
77+
"a_thaliana.pep.fasta:md5,8bd47bdb1cf54e3917c6fe9a45b19da7",
78+
"a_thaliana.gff3:md5,27e5a2d7e9fda9813b5431d37f50a821",
79+
"summary_stats.json:md5,3e322faf84ae2cfb75eda121f98bbe5f"
7780
],
7881
"stable names": [
7982
"annotations",
@@ -95,21 +98,21 @@
9598
"stats": [
9699
{
97100
"ID": "a_thaliana",
98-
"Genes": 252,
99-
"mRNA": 265,
100-
"CDS": 1340,
101-
"Exons": 1340,
102-
"Intron": 1075,
103-
"Non canon splice sites": 18
101+
"Genes": 250,
102+
"mRNA": 264,
103+
"CDS": 1319,
104+
"Exons": 1319,
105+
"Intron": 1055,
106+
"Non canon splice sites": 16
104107
}
105108
]
106109
}
107110
}
108111
],
109112
"meta": {
110113
"nf-test": "0.9.2",
111-
"nextflow": "24.10.5"
114+
"nextflow": "24.10.6"
112115
},
113-
"timestamp": "2025-04-11T12:26:06.229329"
116+
"timestamp": "2025-05-02T18:34:00.928126"
114117
}
115-
}
118+
}

‎tests/stub/main.nf.test.snap

Lines changed: 7 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
"full - stub": {
33
"content": [
44
{
5-
"successful tasks": 126,
5+
"successful tasks": 130,
66
"versions": {
77
"AGAT_CONVERTSPGFF2GTF": {
88
"agat": "v1.4.1"
@@ -61,6 +61,9 @@
6161
"FILTER_BY_ORF_SIZE": {
6262
"agat": "v1.4.3"
6363
},
64+
"FILTER_INVALID_ORFS": {
65+
"gffread": "0.12.7"
66+
},
6467
"FINAL_GFF_CHECK": {
6568
"genometools": "1.6.5"
6669
},
@@ -188,8 +191,8 @@
188191
],
189192
"meta": {
190193
"nf-test": "0.9.2",
191-
"nextflow": "24.10.5"
194+
"nextflow": "24.10.6"
192195
},
193-
"timestamp": "2025-04-11T12:51:09.820302"
196+
"timestamp": "2025-05-02T20:01:32.942669"
194197
}
195-
}
198+
}

‎workflows/genepal.nf

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,6 @@ workflow GENEPAL {
4343

4444
take:
4545
ch_target_assembly
46-
ch_tar_assm_str
4746
ch_is_masked
4847
ch_te_library
4948
ch_braker_annotation
@@ -93,7 +92,6 @@ workflow GENEPAL {
9392
// SUBWORKFLOW: PREPROCESS_RNASEQ
9493
PREPROCESS_RNASEQ(
9594
ch_rna_all_fq,
96-
ch_tar_assm_str,
9795
ch_braker_ex_asm_str,
9896
params.fastqc_skip,
9997
params.fastp_skip,
@@ -138,8 +136,8 @@ workflow GENEPAL {
138136

139137
// SUBWORKFLOW: FASTA_BRAKER3
140138
FASTA_BRAKER3(
139+
ch_valid_target_assembly,
141140
ch_masked_target_assembly,
142-
ch_braker_ex_asm_str,
143141
ch_rnaseq_bam,
144142
ch_ext_prots_fasta,
145143
ch_braker_annotation

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