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Fix parsing issue for reference files with GENCODE v40 and below

Status: Open.

#137 In sheynkman-lab/LRP2;

· JTL-lab opened on Jul 17, 2026

Investigate Singularity HPC config fix for msconvert wine compatibility issue on certain HPCs

Status: Open.

#136 In sheynkman-lab/LRP2;

· JTL-lab opened on Jul 17, 2026

Add support for upload of custom GTF and counts matrix for non-PacBio users

Status: Open.

#124 In sheynkman-lab/LRP2;

· JTL-lab opened on May 28, 2026

Add support for ONT data (alternative to PacBio Isocall for first subworkflow)

Status: Open.

#123 In sheynkman-lab/LRP2;

· JTL-lab opened on May 28, 2026

Add test_dia profile with subsetted test DIA data

Status: Open.

#122 In sheynkman-lab/LRP2;

· JTL-lab opened on May 27, 2026

Fix FRAGPIPE and FRAGPIPE_AUTHENTICATION modules to check fragpipe tools dir

Status: Open.

#63 In sheynkman-lab/LRP2;

· JTL-lab opened on Mar 11, 2026

Fix GUNZIP bug with connection refusal

Status: Open.

#62 In sheynkman-lab/LRP2;

· JTL-lab opened on Mar 11, 2026

Add LRP2 logo

Status: Open.

#61 In sheynkman-lab/LRP2;

· JTL-lab opened on Mar 11, 2026

Add support for NOVEL_PEPTIDES with METAMORPHEUS output

Status: Open.

#56 In sheynkman-lab/LRP2;

· JTL-lab opened on Mar 7, 2026

Determine fix for repeated redundant processes (e.g. GUNZIP) showing in Nextflow summary on pipeline run

Status: Open.

#55 In sheynkman-lab/LRP2;

· JTL-lab opened on Mar 6, 2026

Correct all nf-core linting errors

Status: Open.

#51 In sheynkman-lab/LRP2;

· JTL-lab opened on Mar 4, 2026

Update igenomes default configuration to include version support for RefSeq

Status: Open.

#47 In sheynkman-lab/LRP2;

· JTL-lab opened on Feb 27, 2026