From b8126007d2af1273726bae40ea737a2836159084 Mon Sep 17 00:00:00 2001 From: Thomas Cokelaer Date: Wed, 7 Feb 2024 21:58:30 +0100 Subject: [PATCH] Fix bwa_split --- .github/workflows/apptainer.yml | 1 + .github/workflows/main.yml | 2 ++ README.rst | 1 + pyproject.toml | 2 +- sequana_pipelines/mapper/mapper.rules | 10 +++------- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/apptainer.yml b/.github/workflows/apptainer.yml index f65bcd0..76c8e78 100644 --- a/.github/workflows/apptainer.yml +++ b/.github/workflows/apptainer.yml @@ -49,6 +49,7 @@ jobs: - name: install package itself run: | pip install . + pip install "pulp==2.7.0" --no-deps - name: testing run: | diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 2e18e02..fcc2c77 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -42,6 +42,8 @@ jobs: shell: bash -l {0} run: | pip install . + pip install "pulp==2.7.0" --no-deps + - name: Install dependencies shell: bash -l {0} diff --git a/README.rst b/README.rst index 7652978..a927b24 100644 --- a/README.rst +++ b/README.rst @@ -97,6 +97,7 @@ Changelog ========= ====================================================================== Version Description ========= ====================================================================== +1.2.1 * fix bwa_split bwa aggreate stage (bug fix) 1.2.0 * Implement a bwa_split method to speed up mapping of very large fastq files. 1.1.0 * BAM files are now filtered to remove unmapped reads diff --git a/pyproject.toml b/pyproject.toml index 41114da..2352aa4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [tool.poetry] name = "sequana-mapper" -version = "1.2.0" +version = "1.2.1" description = "A multi-sample mapper to map reads onto a reference" authors = ["Sequana Team"] license = "BSD-3" diff --git a/sequana_pipelines/mapper/mapper.rules b/sequana_pipelines/mapper/mapper.rules index c55a852..bda4356 100644 --- a/sequana_pipelines/mapper/mapper.rules +++ b/sequana_pipelines/mapper/mapper.rules @@ -150,13 +150,9 @@ elif config['general']['mapper'] == 'bwa_split': def aggregate_bwa(wildcards): checkpoint_output = checkpoints.split_fasta.get(**wildcards).output[0] - - splitter = glob.glob(checkpoint_output+ "/*fastq.gz") - # FIXME: hardcoded fastq.gz - splitter = [x.split('.')[-3] for x in splitter if x.endswith(".fastq.gz") and "_R1_" in x] - filenames = expand("{sample}/split/{sample}.sorted.{splitid}.bam", - sample=manager.samples, - splitid=splitter) + splitter = glob.glob(checkpoint_output+ "/*.gz") + splitter = [x.split('.')[-3] for x in splitter if x.endswith(".gz") and "_R1_" in x] + filenames = expand("{{sample}}/split/{{sample}}.sorted.{splitid}.bam", splitid=splitter) return filenames rule bwa_merge: