Open Woodman718 opened 1 month ago
It indeed does not contain correct_barcode_in_fastq.sh
anymore as it was renamed to correct_barcode_from_fastq.sh
. The newer version requires some more arguments than the old one.
There is a newer version of the container, which is used in the latest PUMATAC repo for some code (not for correcting barcodes yet) https://resources.aertslab.org/papers/PUMATAC/PUMATAC_dependencies/cache/vibsinglecellnf-singlecelltoolkit-2024-04-09-62429e9.img
Like for creating fragment files: https://github.com/aertslab/PUMATAC/commit/2ff01a3f8463e0d6b3192772db649e71fd0f362a
//binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/singlecelltoolkit/bin/" : ""
toolParams = params.tools.singlecelltoolkit
process SCTK__BARCODE_CORRECTION {
} However, when I run singularity exec /PUMATAC_tutorial-main/PUMATAC_dependencies/cache/vibsinglecellnf-singlecelltoolkit-2023-04-25-ef1962c.img ls -l /opt/single_cell_toolkit, the output shows:
It does not contain "correct_barcode_in_fastq.sh", but instead has "correct_barcode_from_fastq.sh" and "extract_and_correct_biorad_barcode_in_fastq.sh".
The "correct_barcode_in_fastq.sh" script is present in "vibsinglecellnf-singlecelltoolkit-2022-04-15-16314db.img" and "vibsinglecellnf-singlecelltoolkit-2022-07-07-0638c1d.img" images.