From 69453c3ee920d700bd091caa73b2ba70ce1071b2 Mon Sep 17 00:00:00 2001
From: Maina Vienne <maina.vienne@inrae.fr>
Date: Fri, 21 Jan 2022 18:18:59 +0100
Subject: [PATCH 1/7] Update host_filter.nf
---
modules/host_filter.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/host_filter.nf b/modules/host_filter.nf
index e5f9328..c2b0ba0 100644
--- a/modules/host_filter.nf
+++ b/modules/host_filter.nf
@@ -25,7 +25,7 @@ process HOST_FILTER {
mkdir host_filter_flagstat
samtools flagstat ${sampleId}.bam > ${sampleId}.no_filter.flagstat
samtools flagstat ${sampleId}.without_host.bam >> host_filter_flagstat/${sampleId}.host_filter.flagstat
- bamToFastq -i ${sampleId}.without_host.bam -fq cleaned_${sampleId}_R1.fastq -fq2 cleaned_${sampleId}_R2.fastq
+ bamToFastq -i ${sampleId}.without_host.bam -fq cleaned_${sampleId}_R1.fastq -fq2 cleaned_${sampleId}_R2.fastq
gzip cleaned_${sampleId}_R1.fastq
gzip cleaned_${sampleId}_R2.fastq
rm ${sampleId}.bam
--
GitLab
From 97c1ff29d68677ac9acb99dc3033a47f005ad64f Mon Sep 17 00:00:00 2001
From: Maina Vienne <maina.vienne@inrae.fr>
Date: Mon, 24 Jan 2022 10:20:20 +0100
Subject: [PATCH 2/7] Update host_filter.nf (replace bamtofastq by samtools
fastq )
---
modules/host_filter.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/modules/host_filter.nf b/modules/host_filter.nf
index c2b0ba0..b412799 100644
--- a/modules/host_filter.nf
+++ b/modules/host_filter.nf
@@ -25,10 +25,10 @@ process HOST_FILTER {
mkdir host_filter_flagstat
samtools flagstat ${sampleId}.bam > ${sampleId}.no_filter.flagstat
samtools flagstat ${sampleId}.without_host.bam >> host_filter_flagstat/${sampleId}.host_filter.flagstat
- bamToFastq -i ${sampleId}.without_host.bam -fq cleaned_${sampleId}_R1.fastq -fq2 cleaned_${sampleId}_R2.fastq
- gzip cleaned_${sampleId}_R1.fastq
- gzip cleaned_${sampleId}_R2.fastq
+ samtools sort -n -o ${sampleId}.without_host_sort.bam ${sampleId}.without_host.bam
+ samtools fastq -N -1 cleaned_${sampleId}_R1.fastq.gz -2 cleaned_${sampleId}_R2.fastq.gz ${sampleId}.without_host.bam
rm ${sampleId}.bam
rm ${sampleId}.without_host.bam
+ rm ${sampleId}.without_host_sort.bam
"""
}
\ No newline at end of file
--
GitLab
From a72fc84ca8269084065f877669446a83fc3d5acb Mon Sep 17 00:00:00 2001
From: VIENNE MAINA <maina.vienne@inrae.fr>
Date: Mon, 24 Jan 2022 10:26:22 +0100
Subject: [PATCH 3/7] Update host_filter.nf
---
modules/host_filter.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/modules/host_filter.nf b/modules/host_filter.nf
index b412799..3d87b17 100644
--- a/modules/host_filter.nf
+++ b/modules/host_filter.nf
@@ -26,9 +26,9 @@ process HOST_FILTER {
samtools flagstat ${sampleId}.bam > ${sampleId}.no_filter.flagstat
samtools flagstat ${sampleId}.without_host.bam >> host_filter_flagstat/${sampleId}.host_filter.flagstat
samtools sort -n -o ${sampleId}.without_host_sort.bam ${sampleId}.without_host.bam
- samtools fastq -N -1 cleaned_${sampleId}_R1.fastq.gz -2 cleaned_${sampleId}_R2.fastq.gz ${sampleId}.without_host.bam
+ samtools fastq -N -1 cleaned_${sampleId}_R1.fastq.gz -2 cleaned_${sampleId}_R2.fastq.gz ${sampleId}.without_host_sort.bam
rm ${sampleId}.bam
rm ${sampleId}.without_host.bam
rm ${sampleId}.without_host_sort.bam
"""
-}
\ No newline at end of file
+}
--
GitLab
From a189d131a8c34696731f6ca71489a13b5d6d9a44 Mon Sep 17 00:00:00 2001
From: Jean Mainguy <jean.mainguy@inra.fr>
Date: Tue, 25 Jan 2022 18:04:51 +0100
Subject: [PATCH 4/7] add flagstat report of HiFi reads in multiqc report
---
assets/hifi_multiqc_config.yaml | 3 +++
main.nf | 47 ++++++++++++++++++---------------
modules/multiqc.nf | 6 ++---
modules/read_alignment.nf | 1 +
subworkflows/hifi_reads.nf | 5 +++-
5 files changed, 36 insertions(+), 26 deletions(-)
diff --git a/assets/hifi_multiqc_config.yaml b/assets/hifi_multiqc_config.yaml
index ce6c011..3ca370b 100644
--- a/assets/hifi_multiqc_config.yaml
+++ b/assets/hifi_multiqc_config.yaml
@@ -11,6 +11,9 @@ extra_fn_clean_trim:
- '.contigs'
- '.sort'
+extra_fn_clean_exts:
+ - "_select_contigs_cpm"
+
module_order:
- fastqc:
name: 'FastQC'
diff --git a/main.nf b/main.nf
index 67a944c..fa7ddfb 100644
--- a/main.nf
+++ b/main.nf
@@ -212,20 +212,24 @@ workflow {
// SR only report
ch_cutadapt_report = Channel.empty()
ch_sickle_report = Channel.empty()
- ch_before_filter_report = Channel.empty()
- ch_after_filter_report = Channel.empty()
- ch_fastqc_raw_report = Channel.empty()
+ ch_before_host_filter_report = Channel.empty()
+ ch_after_host_filter_report = Channel.empty()
+
ch_fastqc_clean_report = Channel.empty()
ch_kaiju_report = Channel.empty()
- ch_dedup_report = Channel.empty()
- ch_assembly_report = Channel.empty()
- ch_filtered_report = Channel.empty()
+
// HIFI only report
- ch_hifi_fastqc_report = Channel.empty()
ch_hifi_quast_report = Channel.empty()
// Shared report
+ ch_fastqc_raw_report = Channel.empty()
+ ch_flagstat_report = Channel.empty()
+
+ ch_quast_before_filter_report = Channel.empty()
+ ch_quast_after_filter_report = Channel.empty()
+
+
ch_prokka_report = Channel.empty()
ch_quant_report = Channel.empty()
ch_v_eggnogmapper = Channel.empty()
@@ -253,14 +257,14 @@ workflow {
ch_cutadapt_report = SR.out.cutadapt_report
ch_sickle_report = SR.out.sickle_report
- ch_before_filter_report = SR.out.before_filter_report
- ch_after_filter_report = SR.out.after_filter_report
+ ch_before_host_filter_report = SR.out.before_filter_report
+ ch_after_host_filter_report = SR.out.after_filter_report
ch_fastqc_raw_report = SR.out.fastqc_raw_report
ch_fastqc_clean_report = SR.out.fastqc_clean_report
ch_kaiju_report = SR.out.kaiju_report
- ch_dedup_report = SR.out.dedup_report
- ch_assembly_report = SR.out.assembly_report
- ch_filtered_report = SR.out.filtered_report
+ ch_flagstat_report = SR.out.dedup_report
+ ch_quast_before_filter_report = SR.out.assembly_report
+ ch_quast_after_filter_report = SR.out.filtered_report
}
else if ( params.type.toUpperCase() == "HIFI" ) {
@@ -278,9 +282,10 @@ workflow {
ch_multiqc_config
)
- ch_hifi_fastqc_report = HIFI_READS.out.fastqc_report
- ch_hifi_quast_report = HIFI_READS.out.quast_report
- ch_filtered_report = HIFI_READS.out.quast_report_filtered
+ ch_fastqc_raw_report = HIFI_READS.out.fastqc_report
+ ch_flagstat_report = HIFI_READS.out.flagstat_report
+ ch_quast_before_filter_report = HIFI_READS.out.quast_report
+ ch_quast_after_filter_report = HIFI_READS.out.quast_report_filtered
ch_assembly = HIFI_READS.out.assembly
}
@@ -308,16 +313,14 @@ workflow {
ch_software_versions,
ch_cutadapt_report.collect().ifEmpty([]),
ch_sickle_report.collect().ifEmpty([]),
- ch_before_filter_report.collect().ifEmpty([]),
- ch_after_filter_report.collect().ifEmpty([]),
+ ch_before_host_filter_report.collect().ifEmpty([]),
+ ch_after_host_filter_report.collect().ifEmpty([]),
ch_fastqc_raw_report.collect().ifEmpty([]),
ch_fastqc_clean_report.collect().ifEmpty([]),
ch_kaiju_report.collect().ifEmpty([]),
- ch_dedup_report.collect().ifEmpty([]),
- ch_assembly_report.collect().ifEmpty([]),
- ch_filtered_report.collect().ifEmpty([]),
- ch_hifi_fastqc_report.collect().ifEmpty([]),
- ch_hifi_quast_report.collect().ifEmpty([]),
+ ch_flagstat_report.collect().ifEmpty([]),
+ ch_quast_before_filter_report.collect().ifEmpty([]),
+ ch_quast_after_filter_report.collect().ifEmpty([]),
ch_prokka_report.collect().ifEmpty([]),
ch_quant_report.collect().ifEmpty([])
)
diff --git a/modules/multiqc.nf b/modules/multiqc.nf
index d7334da..01aadbc 100644
--- a/modules/multiqc.nf
+++ b/modules/multiqc.nf
@@ -14,8 +14,6 @@ process MULTIQC {
path dedup_report
path 'quast_primary/*/report.tsv'
path 'quast_filtered/*/report.tsv'
- path hifi_fastqc_report
- path 'quast_hifi/*/report.tsv'
path prokka_report
path quant_report
@@ -27,4 +25,6 @@ process MULTIQC {
"""
multiqc . --config ${multiqc_config} -m custom_content -m fastqc -m cutadapt -m sickle -m kaiju -m quast -m prokka -m featureCounts -m samtools
"""
-}
\ No newline at end of file
+}
+
+
diff --git a/modules/read_alignment.nf b/modules/read_alignment.nf
index 7b86f79..94e6816 100644
--- a/modules/read_alignment.nf
+++ b/modules/read_alignment.nf
@@ -61,6 +61,7 @@ process MINIMAP2_FILTERING {
output:
tuple val(sampleId), path("${sampleId}.idxstats"), emit: sam_idxstat
+ path "${sampleId}.flagstat", emit: sam_flagstat
path "${sampleId}*"
script:
diff --git a/subworkflows/hifi_reads.nf b/subworkflows/hifi_reads.nf
index 373321e..6222c2d 100644
--- a/subworkflows/hifi_reads.nf
+++ b/subworkflows/hifi_reads.nf
@@ -32,6 +32,7 @@ workflow HIFI_READS {
MINIMAP2_FILTERING(ch_contigs_and_reads)
ch_idxstats = MINIMAP2_FILTERING.out.sam_idxstat
+ ch_flagstat = MINIMAP2_FILTERING.out.sam_flagstat
ch_min_contigs_cpm = Channel.value(params.min_contigs_cpm)
@@ -53,15 +54,17 @@ workflow HIFI_READS {
S04_FILTERED_QUAST( ch_assembly )
ch_filtered_report = S04_FILTERED_QUAST.out.report
+
}
emit:
fastqc_report = ch_fastqc_zip
+ flagstat_report = ch_flagstat
quast_report = ch_quast_report
quast_report_filtered = ch_filtered_report
assembly = ch_assembly
}
-
\ No newline at end of file
+
--
GitLab
From 7077b531f3416833a41a695680ab05f49240794d Mon Sep 17 00:00:00 2001
From: Maina Vienne <maina.vienne@inrae.fr>
Date: Wed, 26 Jan 2022 12:37:41 +0100
Subject: [PATCH 5/7] update functional test : expected processes Hifi
---
functional_tests/expected_processes_HiFi.tsv | 12 ++++++------
functional_tests/functions.py | 2 +-
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/functional_tests/expected_processes_HiFi.tsv b/functional_tests/expected_processes_HiFi.tsv
index a4c48ab..d96ce65 100644
--- a/functional_tests/expected_processes_HiFi.tsv
+++ b/functional_tests/expected_processes_HiFi.tsv
@@ -1,6 +1,6 @@
-cmd outputdir DATABASES:INDEX_KAIJU DATABASES:DOWNLOAD_TAXONOMY_DB DATABASES:EGGNOG_MAPPER_DB HIFI_READS:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:MINIMAP2 SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS GET_SOFTWARE_VERSIONS MULTIQC
-mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1
-mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1
-mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump --skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1
-mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1
+cmd outputdir DATABASES:INDEX_KAIJU DATABASES:DOWNLOAD_TAXONOMY_DB DATABASES:EGGNOG_MAPPER_DB HIFI_READS:ASSEMBLY_QUAST HIFI_READS:FASTQC_HIFI HIFI_READS:MINIMAP2_FILTERING HIFI_READS:S03_FILTERING:CHUNK_ASSEMBLY_FILTER HIFI_READS:S03_FILTERING:MERGE_ASSEMBLY_FILTER HIFI_READS:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:MINIMAP2 SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS GET_SOFTWARE_VERSIONS MULTIQC
+mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1
+mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1
+mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump --skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1
+mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1
diff --git a/functional_tests/functions.py b/functional_tests/functions.py
index ba287dc..7c3ec66 100644
--- a/functional_tests/functions.py
+++ b/functional_tests/functions.py
@@ -82,7 +82,7 @@ def files_load(exp_dir, step):
files_list = []
files_dir = path.join(path.abspath(exp_dir), step)
- for file in Path(files_dir).rglob('*.*'):
+ for file in Path(files_dir).rglob('*.[a-z]*'):
files_list.append(path.relpath(file, start = files_dir))
return sorted(files_list)
--
GitLab
From 5b588d44465b95b01a3d2c0ae88219cac06d4596 Mon Sep 17 00:00:00 2001
From: Maina Vienne <maina.vienne@inrae.fr>
Date: Wed, 26 Jan 2022 13:53:14 +0100
Subject: [PATCH 6/7] update doc and help: add '--type' description
---
docs/usage.md | 4 +++-
main.nf | 1 +
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/docs/usage.md b/docs/usage.md
index cdccc87..5a400e1 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -144,10 +144,12 @@ The next parameters can be used when you run metagWGS.
**NOTE:** the specific parameters of the pipeline are indicated by `--` in the command line.
-### 1. Mandatory parameter: `--input`
+### 1. Mandatory parameters:
`--input "<PATH>/samplesheet.csv"`: indicate location of the samplesheet containing paths to the input reads `.fastq/.fastq.gz` and/or assembly `.fa/.fasta` files. For example, `--input "<PATH>/samplesheet.csv"` runs the pipeline with all the `R1.fastq.gz` and `R2.fastq.gz` files available in the indicated `<PATH>`. For a cleaner MultiQC html report at the end of the pipeline, raw data with extensions `_R1` and `_R2` are preferred to those with extensions `_1` and `_2`.
+`--type "SR" or "HIFI"` : indicate the type of the sequencing data, for short-read Illumina data use `"SR"`, for long-read data PacBio HiFi use `"HIFI"`.
+
### 2. `--stop_at_[STEP]` and `--skip_[STEP]` parameters:
By default, all steps of metagWGS will be launched on the input data. From S01_CLEAN_QC to S07_TAXO_AFFI.
diff --git a/main.nf b/main.nf
index fa7ddfb..e4fab3b 100644
--- a/main.nf
+++ b/main.nf
@@ -32,6 +32,7 @@ include { MULTIQC } from './modules/multiqc'
Mandatory arguments:
--input [path] Sample sheet: csv file with samples: sample,fastq_1,fastq_2,fasta[for HIFI]
+ --type Indicate the type of the sequencing data, "SR" : short-read Illumina data use, "HIFI" : long-read PacBio HiFi data
Options:
--
GitLab
From ec2eefa6953fba873cee5289260a9486b24cdc4c Mon Sep 17 00:00:00 2001
From: Jean Mainguy <jean.mainguy@inra.fr>
Date: Tue, 1 Feb 2022 12:28:57 +0100
Subject: [PATCH 7/7] fix plot issue: plot are only generated at the end.
---
bin/aln2taxaffi.py | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/bin/aln2taxaffi.py b/bin/aln2taxaffi.py
index 1478fee..085c4fc 100755
--- a/bin/aln2taxaffi.py
+++ b/bin/aln2taxaffi.py
@@ -524,11 +524,11 @@ def main():
out_contig.write(contig_affi_line)
logging.debug(contig_affi_line)
- with open(query_length_file) as fl:
- nb_total_prot = len([line for line in fl])
- nb_prot_annotated = len(matches)
- plot_taxonomic_assignment(
- output_name, count_rank_affiliation_protein, count_rank_affiliation_contig, nb_total_prot, nb_prot_annotated, nb_prot_assigned)
+ with open(query_length_file) as fl:
+ nb_total_prot = len([line for line in fl])
+ nb_prot_annotated = len(matches)
+ plot_taxonomic_assignment(
+ output_name, count_rank_affiliation_protein, count_rank_affiliation_contig, nb_total_prot, nb_prot_annotated, nb_prot_assigned)
if __name__ == '__main__':
--
GitLab