Script "correct_barcode_in_fastq.sh" missing in newer image

[Woodman718]

cat PUMATAC_tutorial-main/PUMATAC/src/singlecelltoolkit/processes/barcode_correction.nf
nextflow.enable.dsl=2

//binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/singlecelltoolkit/bin/" : ""

toolParams = params.tools.singlecelltoolkit

process SCTK__BARCODE_CORRECTION {

container toolParams.container
label 'compute_resources__sctk_barcode'

input:
    tuple val(sampleId),
          val(technology),
          path(fastq_PE1),
          path(fastq_bc),
          path(fastq_PE2),
          path(bc_whitelist)

output:
    tuple val(sampleId),
          val(technology),
          path(fastq_PE1),
          path("${sampleId}_bc_corrected.fastq.gz"),
          path(fastq_PE2),
          path("${sampleId}_bc_corrected.fastq.gz.corrected.bc_stats.tsv")

script:
    def sampleParams = params.parseConfig(sampleId, params.global, toolParams.barcode_correction)
    processParams = sampleParams.local
    """
    correct_barcode_in_fastq.sh \
        ${bc_whitelist} \
        ${fastq_bc} \
        ${sampleId}_bc_corrected.fastq.gz \
        ${processParams.max_mismatches} \
        ${processParams.min_frac_bcs_to_find}
    """

}
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:

README.md
add_corrected_barcode_to_read_name.sh
barcard
barcode_10x_scatac_fastqs.sh
calculate_saturation_10x_samples.py
calculate_saturation_from_fragments.py
correct_barcode_from_fastq.seq
correct_barcode_from_fastq.sh
create_fragments_file
create_scifi_rna_barcode_fastq_for_star_solo.sh
extract_and_correct_biorad_barcode_in_fastq.seq
extract_and_correct_biorad_barcode_in_fastq.sh
extract_and_correct_scalebio_atac_barcode_from_fastq.seq
extract_and_correct_scalebio_atac_barcode_from_fastq.sh
extract_and_correct_scifi_rna_barcode_from_fastq.seq
extract_hydrop_atac_barcode_from_R2_fastq.sh
filter_star_solo_raw_count_matrix.py
fix_sra_fastq.sh
mark_or_remove_duplicates_per_barcode.sh
run_seq_program.sh
seq_lib
test

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.

[ghuls]

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: aertslab/PUMATAC@2ff01a3