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.

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

Add pear #10

Merged
merged 17 commits into from
Feb 2, 2024
Merged
Show file tree
Hide file tree
Changes from 1 commit
Commits
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
Prev Previous commit
Next Next commit
add requirements
  • Loading branch information
KaiWaldrant committed Jan 29, 2024
commit c86e885e5a106dca20643f6f99bb6ad52eda5d84
11 changes: 4 additions & 7 deletions src/pear/config.vsh.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,10 @@ functionality:
documentatoin: https://cme.h-its.org/exelixis/web/software/pear/doc.html
KaiWaldrant marked this conversation as resolved.
Show resolved Hide resolved
reference: doi:10.1093/bioinformatics/btt593
licence: "['Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported']"
KaiWaldrant marked this conversation as resolved.
Show resolved Hide resolved
requirements:
cpus: 1
KaiWaldrant marked this conversation as resolved.
Show resolved Hide resolved
memory: 4GB
KaiWaldrant marked this conversation as resolved.
Show resolved Hide resolved
commands: [ pear , gzip ]
argument_groups:
- name: Inputs
arguments:
Expand Down Expand Up @@ -122,13 +126,6 @@ functionality:
Specify the upper bound for the resulting quality score. If set to zero, capping is disabled.
required: false
default: 40
- name: --threads
alternatives: -j
type: integer
description: |
Number of threads to use.
required: false
example: 1
- name: --nbase
alternatives: -z
type: boolean_true
Expand Down
2 changes: 1 addition & 1 deletion src/pear/script.sh
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ pear \
${par_phred_base:+-b "${par_phred_base}"} \
${par_memory:+-y "${par_memory}"} \
rcannood marked this conversation as resolved.
Show resolved Hide resolved
${par_cap:+-c "${par_cap}"} \
${par_threads:+-j "${par_threads}"} \
${meta_cpus:+-j "${meta_cpus}"} \
${par_emperical_freqs:+-e} \
${par_nbase:+-z}

Expand Down
1 change: 0 additions & 1 deletion src/pear/test.sh
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@ echo "> Run PEAR"
--reverse_fastq "$dir_in/reads.right.fq.gz" \
--output "test" \
--p_value 0.01 \
--threads 4 \
--memory "4G"

echo ">> Checking output"
Expand Down