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spikein_bowtie2 parameter incorrectly assigned to iGenomes Bowtie index when using local spikein_fasta
bugSomething isn't workingSomething isn't workingStatus: Open.#313 In nf-core/cutandrun;Resource allocations for several tools are excessive
bugSomething isn't workingSomething isn't workingStatus: Open.#310 In nf-core/cutandrun;Nextflow 25.10.4 fails with Cannot invoke method optional() on null object in TRIMGALORE module (nf-core/cutandrun v3.2.2)
bugSomething isn't workingSomething isn't workingStatus: Open.#309 In nf-core/cutandrun;- Status: Open.#308 In nf-core/cutandrun;
matplotlib temp file
bugSomething isn't workingSomething isn't workingStatus: Open.#305 In nf-core/cutandrun;duplicates are always removed
bugSomething isn't workingSomething isn't workingStatus: Open.#304 In nf-core/cutandrun;Pipeline failure if a sample has zero alignments
bugSomething isn't workingSomething isn't workingStatus: Open.#303 In nf-core/cutandrun;test run TRIMGALORE error
bugSomething isn't workingSomething isn't workingStatus: Open.#301 In nf-core/cutandrun;TODO list for 3.3.0 release
enhancementImprovement for existing functionalityImprovement for existing functionalityStatus: Open.Consesus peaks
enhancementImprovement for existing functionalityImprovement for existing functionalityStatus: Open.#298 In nf-core/cutandrun;cutandrun pipeline reflects density across individual reads rather than read pairs (?)
bugSomething isn't workingSomething isn't workingStatus: Open.#297 In nf-core/cutandrun;NFCORE_CUTANDRUN:CUTANDRUN:FILTER_READS:SAMTOOLS_VIEW
bugSomething isn't workingSomething isn't workingStatus: Open.#295 In nf-core/cutandrun;