Merge pull request #19 from cokelaer/main

Fix bwa_split

.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: |

.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}

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

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"

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: