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New DSL2 main.nf isn't processing bam files

Status: Open.

#45 In nebiolabs/EM-seq;

· kellywuthrich opened on Dec 19, 2025

Aggregation needs the pre-adapter trimmed (post-downsampled) ubams for num_reads_used

Status: Open.

#32 In nebiolabs/EM-seq;

· mattsoup opened on Jul 8, 2025

IndexOutOfBoundsException: fromIndex = -1

Status: Open.

#31 In nebiolabs/EM-seq;

· charles-gumbi opened on Jun 18, 2025

Add picard markduplicates report to mulitqc

Status: Open.

#29 In nebiolabs/EM-seq;

· bwlang opened on May 27, 2025

Aggregation needs either untrimmed fastqs or the original (post-downsampled) ubam

Status: Open.

#19 In nebiolabs/EM-seq;

· mattsoup opened on Mar 15, 2025

Output files should go to users' galaxy import directory

Status: Open.

#18 In nebiolabs/EM-seq;

· mattsoup opened on Mar 14, 2025

Trouble finding index

Status: Open.

#16 In nebiolabs/EM-seq;

· matthewangel opened on Mar 6, 2025

fastq/bam header parsing when unexpected format

Status: Open.

#15 In nebiolabs/EM-seq;

· lnblum opened on Jan 10, 2025

move this to an accessory script?

Status: Open.

#14 In nebiolabs/EM-seq;

· bwlang opened on Dec 25, 2024

fix dsl2 version to handle fastq.gz files

Status: Open.

#12 In nebiolabs/EM-seq;

· bwlang opened on Feb 20, 2024

Fetch common genome files for combination with controls

Status: Open.

#11 In nebiolabs/EM-seq;

· bwlang opened on Sep 7, 2023