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isugifNF / polishCLR

A nextflow pipeline for polishing CLR assemblies
https://isugifnf.github.io/polishCLR/
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feat: check software dependencies #44

Closed j23414 closed 1 year ago

j23414 commented 1 year ago

Description

Added a --check_software flag to print out paths to software dependencies and their versions:

Issues

Related to issues: https://github.com/isugifNF/polishCLR/issues/22

Testing

Assuming reviewer has a working install of nextflow nextflow -version

Can test via:

nextflow run isugifNF/polishCLR -r check_software \
  --check_software \
  -profile local

Which will print output similar to:

N E X T F L O W  ~  version 22.04.5
Launching `main.nf` [marvelous_woese] DSL2 - revision: 6705f3a174
executor >  local (1)
[9c/7800d2] process > check_software [100%] 1 of 1 ✔ ===== Dependencies check =====
parallel   .... good.  GNU parallel 20220922
bzcat      .... good.  bzip2, a block-sorting file compressor. Version 1.0.8, 13-Jul-2019.
pigz       .... good.  pigz 2.6
meryl      .... good.  meryl 1.3
pbmm2      .... good.  pbmm2 1.7.0 (commit 1.7.0)
minimap2   .... good.  2.24-r1122
samtools   .... good.  samtools 1.12
gcpp       .... good.  polishCLR/work/9c/7800d23b6b3aa959b3f64f6b9ed645/.command.sh: line 11: polishCLR/env/polishCLR_env/bin/gcpp: cannot execute binary file
bwa-mem2    .... need to install.
freebayes  .... good.  version: v1.3.5
bcftools   .... good.  bcftools 1.12
merfin     .... good.  merfin 1.0
pbcstat    .... good.  Usage: aa_pb [options] <PAF_FILE> ...
calcuts    .... good.  Usage: calcuts [<options>] <STAT> ...
split_fa   .... good.  Usage: split_fa [<options>] <STAT> ...
purge_dups .... good.  Version: 1.2.5
get_seqs   .... good.  Usage: get_seqs [<options>] <DUPs.BED> <FASTA>
gzip       .... good.  gzip 1.12
busco      .... need to install.