Pramod Rao Budramane

### What version of rules_go are you using? 0.46.0 ### What version of gazelle are you using? 0.34.0 ### What version of Bazel are you using? 7.1.0 ### Does this...

Improve qualimap execution time

3

### Description of feature The `qualimap` tool sorts the input bam file by read-name and does so in a single-threaded manner. On a dataset that I'm using, the total execution...

Parallel processing of paired-end fastq files

2

From my understanding of the code, in paired-end processing, both fastq input files could be processed parallelly, but they are currently sequential. Is this correct? If so, I could take...

Add peek method for SortingLongCollections

1

### Description of the issue: Currently, the SortingLongCollection does not provide a method to peek the value of the top-most element. This makes it impossible to perform some processing on-top...

Number of cores calculation for Trimgalore

1

### Description of the bug As discussed in this [issue](https://github.com/nf-core/atacseq/pull/65), the calculation for actual number of cores used by Trimgalore is convoluted. The current calculation is present in [this code](https://github.com/nf-core/rnaseq/blob/b96a75361a4f1d49aa969a2b1c68e3e607de06e8/modules/nf-core/trimgalore/main.nf#L30)....