Script "correct_barcode_in_fastq.sh" missing in newer image #5
Description
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.