Skip to content

Commit 5d12197

Browse files
cimendescimendes
authored
Merge pull request #25 from B-UMMI/remove_bcalm2
remove BCALM2 from workflow
2 parents a49bc93 + dee32c2 commit 5d12197

File tree

8 files changed

+8
-93
lines changed

8 files changed

+8
-93
lines changed

‎.github/workflows/ci_nextflow.yml

+2-2
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,7 @@ jobs:
2323
run: |
2424
nextflow run ${GITHUB_WORKSPACE} -profile docker --fastq "test/data/tiny_{1,2}.*" \
2525
--reference "test/data/tiny_reference.fasta" --max_cpus 2 --max_memory 4.GB \
26-
--abyss false --bcalm false --gatb_minia false --idba false --metahipmer2 false \
26+
--abyss false --gatb_minia false --idba false --metahipmer2 false \
2727
--minia false --megahit false --metaspades false --spades false --unicycler false \
2828
--velvetoptimiser false
2929
FILE=report/index.html
@@ -50,7 +50,7 @@ jobs:
5050
run: |
5151
nextflow run ${GITHUB_WORKSPACE} -profile singularity --fastq "test/data/tiny_{1,2}.*" \
5252
--reference "test/data/tiny_reference.fasta" --max_cpus 2 --max_memory 4.GB \
53-
--abyss false --bcalm false --gatb_minia false --idba false --metahipmer2 false \
53+
--abyss false --gatb_minia false --idba false --metahipmer2 false \
5454
--minia false --megahit false --metaspades false --spades false --unicycler false \
5555
--velvetoptimiser false
5656
FILE=report/index.html

‎conf/containers.config

+1-4
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,10 @@
11
process {
22
withName: REFORMAT {
3-
container = "pcerqueira/bbtools:38.44"
3+
container = "pcerqueira/bbtools:38.44"
44
}
55
withName: ABYSS {
66
container = "cimendes/abyss:2.3.1-1"
77
}
8-
withName: BCALM2 {
9-
container = "cimendes/bcalm:2.2.3-1"
10-
}
118
withName: GATBMINIAPIPELINE {
129
container = "cimendes/gatb-minia-pipeline:31.07.2020-1"
1310
}

‎conf/params.config

-4
Original file line numberDiff line numberDiff line change
@@ -17,10 +17,6 @@ params {
1717
abyssKmerSize = 96
1818
abyssBloomSize = '2G'
1919

20-
//BCALM2
21-
bcalm = false
22-
bcalmKmerSize = 31
23-
2420
//GATB Minia Pipeline
2521
gatb_minia = true
2622
gatbKmerSize = '21,61,101,141,181'

‎docker/bcalm/Dockerfile

-29
This file was deleted.

‎lib/CheckParams.groovy

+2-3
Original file line numberDiff line numberDiff line change
@@ -9,11 +9,10 @@ class Params {
99
if (params.fastq instanceof Boolean) {print_error("'--fastq' must be a path pattern. Provided value: '$params.fastq'")}
1010

1111
// assembler skipping
12-
if (!params.abyss && !params.bcalm && !params.gatb_minia && !params.idba && !params.metahipmer2 && !params.minia && !params.megahit && !params.metaspades && !params.spades && !params.skesa && !params.unicycler && !params.velvetoptimiser) {print_error("All assembly processes set to false. Exiting.")}
12+
if (!params.abyss && !params.gatb_minia && !params.idba && !params.metahipmer2 && !params.minia && !params.megahit && !params.metaspades && !params.spades && !params.skesa && !params.unicycler && !params.velvetoptimiser) {print_error("All assembly processes set to false. Exiting.")}
1313

1414
// assembler parameters
15-
if (!params.abyssKmerSize.toString().isNumber()) {print_error("'--bcalmKmerSize' parameter must be a number. Provided value: '$params.abyssKmerSize'")}
16-
if (!params.bcalmKmerSize.toString().isNumber()) {print_error("'--bcalmKmerSize' parameter must be a number. Provided value: '$params.bcalmKmerSize'")}
15+
if (!params.abyssKmerSize.toString().isNumber()) {print_error("'--abyssKmerSize' parameter must be a number. Provided value: '$params.abyssKmerSize'")}
1716
if (!params.gatb_besst_iter.toString().isNumber()) {print_error("'--gatb_besst_iter' parameter must be a number. Provided value: '$params.gatb_besst_iter'")}
1817
if (params.metaspadesKmerSize.toString().split(" ").size() <= 1) {if (params.metaspadesKmerSize.toString() != 'auto') {print_error("'--metaspadesKmerSize' parameter must be a sequence of space separated numbers or 'auto'. Provided value: '$params.metaspadesKmerSize'")}}
1918
if (params.spadesKmerSize.toString().split(" ").size() <= 1) {if (params.spadesKmerSize.toString() != 'auto'){print_error("'--spadesKmerSize' parameter must be a sequence of space separated numbers or 'auto'. Provided value: '$params.spadesKmerSize'")}}

‎lib/Helper.groovy

-5
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,6 @@ class Help {
1212
println ""
1313
int nsamples = info.fastq / 2
1414
println " Input FastQ : $nsamples"
15-
println " Reference file : $info.referece"
1615
println " Reports are found in : ./reports"
1716
println " Results are found in : ./results"
1817
println " Profile : $profile"
@@ -65,10 +64,6 @@ class Help {
6564
println " --abyssBloomSize Bloom filter size for the ABySS assembler."
6665
println " It must be a sting with a value and an unit."
6766
println " (default: $params.abyssBloomSize)"
68-
println " --bcalm Boolean controling the execution of the BCALM2 assembler."
69-
println " (default: $params.bcalm)"
70-
println " --bcalmKmerSize K-mer size for the BCALM2 assembler, as an intiger."
71-
println " (default $params.bcalmKmerSize)"
7267
println " --gatb_minia Boolean controling the execution of the GATB Minia Pipeline assembler."
7368
println " (default: $params.gatb_minia)"
7469
println " --gatbKmerSize K-mer sizes for the GATB Minia Pipeline assembler."

‎main.nf

+1-5
Original file line numberDiff line numberDiff line change
@@ -49,11 +49,7 @@ if (params.containsKey('fastq')) {
4949
infoMap.put('fastq', file(params.fastq).size())
5050
}
5151
if (params.containsKey('reference')) {
52-
if (file(params.reference) instanceof LinkedList) {
53-
infoMap.put('reference', file(params.reference).size())
54-
} else {
55-
infoMap.put('fasta', 1)
56-
}
52+
infoMap.put('reference', file(params.reference).getName())
5753
}
5854

5955
Help.start_info(infoMap, "$workflow.start", "$workflow.profile", "$workflow.manifest.version")

‎modules/assembly/assembly.nf

+2-41
Original file line numberDiff line numberDiff line change
@@ -53,41 +53,6 @@ process ABYSS {
5353
"""
5454
}
5555

56-
process BCALM2 {
57-
58-
tag { sample_id }
59-
label 'process_assembly'
60-
publishDir "results/$sample_id/assembly/bcalm2/"
61-
62-
when:
63-
params.bcalm
64-
65-
input:
66-
tuple val(sample_id), path(fastq)
67-
val KmerSize
68-
69-
output:
70-
tuple val(sample_id), val('BCALM2'), path('*_BCALM2.fasta'), emit: assembly
71-
path('.*version'), emit: version
72-
73-
script:
74-
"""
75-
ls -1 $fastq > list_reads
76-
bcalm -version | head -n 1 | awk -F ', ' '{print \$2}' | awk -F ' ' '{print \$2}' | awk -F 'v' '{print \$2}' \
77-
> .${sample_id}_BCALM2_version
78-
{
79-
bcalm -in list_reads -out ${sample_id} -kmer-size $KmerSize
80-
mv ${sample_id}.unitigs.fa ${sample_id}_BCALM2.fasta
81-
echo pass > .status
82-
} || {
83-
echo fail > .status
84-
:> ${sample_id}_BCALM2.fasta
85-
}
86-
# remove temp files
87-
rm list_reads *.fa || true
88-
"""
89-
}
90-
9156
process GATBMINIAPIPELINE {
9257

9358
tag { sample_id }
@@ -440,7 +405,6 @@ workflow assembly_wf {
440405

441406
abyssKmerSize = Channel.value(params.abyssKmerSize)
442407
abyssBloomSize = Channel.value(params.abyssBloomSize)
443-
bcalmKmerSize = Channel.value(params.bcalmKmerSize)
444408
gatbKmerSize = Channel.value(params.gatbKmerSize)
445409
GATB_error_correction = params.gatb_error_correction ? 'true' : 'false'
446410
gatb_besst_iter = Channel.value(params.gatb_besst_iter)
@@ -456,7 +420,6 @@ workflow assembly_wf {
456420
main:
457421
REFORMAT(IN_fastq_raw)
458422
ABYSS(IN_fastq_raw, abyssKmerSize, abyssBloomSize)
459-
BCALM2(IN_fastq_raw, bcalmKmerSize)
460423
GATBMINIAPIPELINE(IN_fastq_raw, gatbKmerSize, GATB_error_correction, gatb_besst_iter)
461424
IDBA(REFORMAT.out)
462425
MEGAHIT(IN_fastq_raw, megahitKmerSize)
@@ -469,8 +432,7 @@ workflow assembly_wf {
469432
VELVETOPTIMISER(IN_fastq_raw)
470433

471434
emit:
472-
all_assemblies = ABYSS.out.assembly | mix(BCALM2.out.assembly,
473-
GATBMINIAPIPELINE.out.assembly,
435+
all_assemblies = ABYSS.out.assembly | mix(GATBMINIAPIPELINE.out.assembly,
474436
IDBA.out.assembly,
475437
MEGAHIT.out.assembly,
476438
METAHIPMER2.out.assembly,
@@ -480,8 +442,7 @@ workflow assembly_wf {
480442
SPADES.out.assembly,
481443
UNICYCLER.out.assembly,
482444
VELVETOPTIMISER.out.assembly)
483-
all_versions = ABYSS.out.version | mix(BCALM2.out.version,
484-
GATBMINIAPIPELINE.out.version,
445+
all_versions = ABYSS.out.version | mix(GATBMINIAPIPELINE.out.version,
485446
IDBA.out.version,
486447
MEGAHIT.out.version,
487448
METAHIPMER2.out.version,

0 commit comments

Comments
 (0)