Bowtie2 mapping script in Nextflow Pipeline fails to execute

[unikill066]

I have a Nextflow script that triggers multiple processes, one of which is a mapping step that utilizes Bowtie2. When I run this mapping process directly using the script or as a standalone command, the mapped files are generated successfully. However, when I attempt to run it through the Nextflow pipeline, it doesn't seem to execute.

Nextflow-run [DOES NOT WORK]:

/path/to/pipeline/bowtie2_fq_2bam.sh /path/to/pipeline/trim_output /path/to/pipeline/samples.txt /path/to/pipeline hg38
2024-08-12 12:00:56 276-2_S1_L001 Running bowtie2 mapping ...
(bowtie2 --very-sensitive -I 0 -X 1000 -x hg38 -1 "/path/to/pipeline/trim_output/276-2_S1_L001_R1_001_val_1.fq.gz" -2 "/path/to/pipeline/trim_output/276-2_S1_L001_R2_001_val_2.fq.gz" --fr | samtools view -q 30 -f 2 -F 4 -h - | grep -v 'chrM' | samtools view -bS - > "/path/to/pipeline/bowtie_output/276-2_S1_L001_filtered_output.bam") 2> "/path/to/pipeline/bowtie_output/log/276-2_S1_L001_mapping_step.log"
Error during bowtie2 mapping for 276-2_S1_L001

Command-line [WORKS]:

./bowtie2_fq_2bam.sh "/path/to/pipeline/trim_output" "/path/to/pipeline/samples.txt" "/path/to/pipeline" "hg38"

Individual command [WORKS]:

bamtools sort -in "${BOWTIE_OUTPUT_PATH}/${LIBR_NAME}_filtered_output.bam" -out "${BOWTIE_OUTPUT_PATH}/${LIBR_NAME}_filtered_output_sort.bam"
    bamtools filter -in "${BOWTIE_OUTPUT_PATH}/${LIBR_NAME}_filtered_output_sort.bam" -out "${BOWTIE_OUTPUT_PATH}/${LIBR_NAME}_filtered_output_filt.bam" -mapQuality ">=30" -isProperPair true
    samtools view -h "${BOWTIE_OUTPUT_PATH}/${LIBR_NAME}_filtered_output_filt.bam" | grep -v "chrM" | samtools view -b -o "${BOWTIE_OUTPUT_PATH}/${LIBR_NAME}_filtered_output.bam"
    rm "${BOWTIE_OUTPUT_PATH}/${LIBR_NAME}_filtered_output_sort.bam" "${BOWTIE_OUTPUT_PATH}/${LIBR_NAME}_filtered_output_filt.bam"

[pditommaso]

Check the .command.sh generated by nextflow and run it by using bash /your/task/work/dir/.command.run to debug it