Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

85 prokka module can get after modules stuck if the header file longer than 20 and not separated by tab or space #89

Merged
merged 3 commits into from
Mar 3, 2023
Merged

85 prokka module can get after modules stuck if the header file longer than 20 and not separated by tab or space #89

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
f4bd090
add awk command to clean big fasta headers
fmalmeida Mar 3, 2023
ef60f9f
add awk statement to clean big fasta headers
fmalmeida Mar 3, 2023
e25e8a2
update bakta version
fmalmeida Mar 3, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion conf/defaults.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -177,7 +177,7 @@ params {
// but can eventually be used by users
unicycler_version = '0.4.8--py38h8162308_3'
flye_version = '2.9--py39h39abbe0_0'
bakta_version = '1.6.1--pyhdfd78af_0'
bakta_version = '1.7.0--pyhdfd78af_1'

// Max resource options
max_memory = '20.GB'
Expand Down
2 changes: 1 addition & 1 deletion docs/config.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -192,7 +192,7 @@ params {
// but can eventually be used by users
unicycler_version = '0.4.8--py38h8162308_3'
flye_version = '2.9--py39h39abbe0_0'
bakta_version = '1.6.1--pyhdfd78af_0'
bakta_version = '1.7.0--pyhdfd78af_1'

// Max resource options
max_memory = '20.GB'
Expand Down
2 changes: 1 addition & 1 deletion docs/manual.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,7 @@ Users can now select the version of the non-core tools Bakta, Unicyler and Flye.

| Parameter | Default | Description |
| :-------- | :------ | :---------- |
| `--bakta_version` | 1.6.1--pyhdfd78af_0 | Bakta tool version |
| `--bakta_version` | 1.7.0--pyhdfd78af_1 | Bakta tool version |
| `--flye_version` | 2.9--py39h39abbe0_0 | Flye tool version |
| `--unicycler_version` | 0.4.8--py38h8162308_3 | Unicycler tool version |

Expand Down
11 changes: 7 additions & 4 deletions modules/generic/bakta.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@ process BAKTA {
tag "${prefix}"
label = [ 'process_medium', 'error_retry' ]

conda "bioconda::bakta=1.6.1"
conda "bioconda::bakta=1.7.0"
container "${ workflow.containerEngine == 'singularity' ?
'https://depot.galaxyproject.org/singularity/bakta:1.6.1--pyhdfd78af_0' :
'quay.io/biocontainers/bakta:1.6.1--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/bakta:1.7.0--pyhdfd78af_1' :
'quay.io/biocontainers/bakta:1.7.0--pyhdfd78af_1' }"

input:
tuple val(prefix), val(entrypoint), file(sread1), file(sread2), file(sreads), file(lreads), val(lr_type), file(fast5), file(assembly), val(resfinder_species)
Expand Down Expand Up @@ -38,6 +38,9 @@ process BAKTA {
# Save bakta version
bakta --version &> bakta_version.txt ;

# clean headers char limit
awk '{ if (\$0 ~ />/) print substr(\$0,1,21) ; else print \$0 }' $assembly > cleaned_header.fasta

# Run bakta
bakta \\
--output annotation \\
Expand All @@ -46,7 +49,7 @@ process BAKTA {
--prefix ${prefix} \\
--strain '${prefix}' \\
--db $bakta_db \\
$assembly
cleaned_header.fasta

# fix fasta headers
cut -f 1 -d ' ' annotation/${prefix}.fna > tmp.fa
Expand Down
21 changes: 13 additions & 8 deletions modules/generic/prokka.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
process PROKKA {
publishDir "${params.output}/${prefix}", mode: 'copy', saveAs: { filename ->
if (filename.indexOf("_version.txt") > 0) "tools_versioning/$filename"
else if (filename == "annotation") "$filename"
else null
if (filename.indexOf("_version.txt") > 0) "tools_versioning/$filename"
else if (filename == "annotation") "$filename"
else null
}
tag "${prefix}"
label = [ 'process_medium' ]
Expand Down Expand Up @@ -31,11 +31,13 @@ process PROKKA {
path('prokka_version.txt'), emit: version

script:
kingdom = (params.prokka_kingdom) ? "--kingdom ${params.prokka_kingdom}" : ''
gcode = (params.prokka_genetic_code) ? "--gcode ${params.prokka_genetic_code}" : ''
rnammer = (params.prokka_use_rnammer) ? "--rnammer" : ''
models = (params.prokka_use_pgap) ? "PGAP_NCBI.hmm" : "TIGRFAMs_15.0.hmm"
kingdom = (params.prokka_kingdom) ? "--kingdom ${params.prokka_kingdom}" : ''
gcode = (params.prokka_genetic_code) ? "--gcode ${params.prokka_genetic_code}" : ''
rnammer = (params.prokka_use_rnammer) ? "--rnammer" : ''
models = (params.prokka_use_pgap) ? "PGAP_NCBI.hmm" : "TIGRFAMs_15.0.hmm"
"""
#!/usr/bin/env bash

# save prokka version
prokka -v &> prokka_version.txt ;

Expand All @@ -50,6 +52,9 @@ process PROKKA {
# hmmpress
( cd prokka_db/hmm/ ; for i in *.hmm ; do hmmpress -f \$i ; done )

# clean headers char limit
awk '{ if (\$0 ~ />/) print substr(\$0,1,21) ; else print \$0 }' $assembly > cleaned_header.fasta

# run prokka
prokka \\
--dbdir prokka_db \\
Expand All @@ -61,7 +66,7 @@ process PROKKA {
--genus '' \\
--species '' \\
--strain \"${prefix}\" \\
$assembly
cleaned_header.fasta

# remove tmp dir to gain space
rm -r prokka_db
Expand Down
2 changes: 1 addition & 1 deletion nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -336,7 +336,7 @@
"bakta_version": {
"type": "string",
"description": "Select quay.io image tag for tool",
"default": "1.6.1--pyhdfd78af_0"
"default": "1.7.0--pyhdfd78af_1"
}
}
},
Expand Down