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Now removing comments from FASTA file before feeding it to BRAKER #32

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May 13, 2024
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Now removing comments from FASTA file before feeding it to BRAKER #32

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18 changes: 18 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,24 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## 0.3.2 - [13-May-2024]

### `Added`

### `Fixed`

1. Increased time limit for REPEATMODELER_REPEATMODELER to 5 days
2. Now removing comments from fasta file before feeding it to BRAKER added tests for the perl one liner
3. Fixed CHANGELOG version check failure in `version_check.sh`
4. Increased the SLURM job time limit to 14 days

### `Dependencies`

1. NextFlow!>=23.04.4
2. nf-validation=1.1.3

### `Deprecated`

## 0.3.1 - [10-May-2024]

### `Added`
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10 changes: 5 additions & 5 deletions conf/base.config
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Expand Up @@ -66,21 +66,21 @@ process {
memory = { check_max( 200.GB * task.attempt, 'memory' ) }
}

withName:REPEATMODELER_REPEATMODELER {
time = { check_max( 3.days * task.attempt, 'time' ) }
withName:EGGNOGMAPPER {
time = { check_max( 1.day * task.attempt, 'time' ) }
}
withName:REPEATMASKER {
time = { check_max( 2.days * task.attempt, 'time' ) }
}
withName:REPEATMODELER_REPEATMODELER {
time = { check_max( 5.days * task.attempt, 'time' ) }
}
withName:EDTA_EDTA {
time = { check_max( 7.days * task.attempt, 'time' ) }
}
withName:BRAKER3 {
time = { check_max( 7.days * task.attempt, 'time' ) }
}
withName:EGGNOGMAPPER {
time = { check_max( 1.day * task.attempt, 'time' ) }
}
withName:CUSTOM_DUMPSOFTWAREVERSIONS {
cache = false
}
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6 changes: 5 additions & 1 deletion modules/kherronism/braker3/main.nf
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Expand Up @@ -42,8 +42,12 @@ process BRAKER3 {
"""
cp -r /usr/share/augustus/config augustus_config

perl -p -e 's/^(>\\S+).*\$/\$1/' \\
${fasta} \\
> ${prefix}.name.only.genome.masked.fasta

braker.pl \\
--genome ${fasta} \\
--genome ${prefix}.name.only.genome.masked.fasta \\
${new_species} \\
--workingdir ${prefix} \\
--AUGUSTUS_CONFIG_PATH "\$(pwd)/augustus_config" \\
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4 changes: 4 additions & 0 deletions modules/kherronism/braker3/tests/name.only.sh
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@@ -0,0 +1,4 @@
#!/usr/bin/env bash

perl -p -e 's/^(>\S+).*$/$1/' \
modules/kherronism/braker3/tests/test.fa
16 changes: 16 additions & 0 deletions modules/kherronism/braker3/tests/test.fa
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@@ -0,0 +1,16 @@
>chr1 This is with four spaces and a space and a tab
AAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
>chr2 This is with four spaces
TAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAA
CCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCT
AAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
>chr3 This is with a single space
TAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAA
CCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCT
>chrX
AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACC
CTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAA
>chrY This desc is with tab and another tab | and a vertical slash
AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACC
CTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAA
2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -58,7 +58,7 @@ manifest {
description = """A NextFlow pipeline for pan-genome annotation"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.4'
version = '0.3.1'
version = '0.3.2'
doi = ''
}

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2 changes: 1 addition & 1 deletion pfr_pangene
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Expand Up @@ -2,7 +2,7 @@


#SBATCH --job-name PANGENE
#SBATCH --time=7-00:00:00
#SBATCH --time=14-00:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
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2 changes: 1 addition & 1 deletion version_check.sh
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Expand Up @@ -4,5 +4,5 @@ config_version=$(sed -n "s/.*version.*= '\(.*\)'.*/\1/p" nextflow.config)

# Check CHANGELOG version

grep "## $config_version - " CHANGELOG.md >/dev/null \
head -n 10 CHANGELOG.md | grep "## $config_version - " >/dev/null \
|| (echo 'Failed to match CHANGELOG version'; exit 1)
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