Channel 'star_index' used twice

[ChillyMomo709]

Hi,

I ran the following using the star_index of the testdata (made by default run settings of STAR genomeGenerate)

nextflow run nf-core/scrnaseq --reads 'data/S10_L001/*_R{1,2}*.fastq.gz' -profile docker -r 1.0.0 --aligner star --type 10x --chemistry V3 --fasta data/references/GRCm38.p6.genome.chr19/GRCm38.p6.genome.chr19.fa --gtf data/references/GRCm38.p6.genome.chr19/gencode.vM19.annotation.chr19.gtf --max_memory 6.GB --max_cpus 2 --star_index data/references/GRCm38.p6.genome.chr19/star/

I get the following error:

Channelstar_indexhas been used twice as an output by processmakeSTARindex` and another operator

-- Check script '/root/.nextflow/assets/nf-core/scrnaseq/main.nf' at line: 365 or see '.nextflow.log' file for more details`

Information output: N E X T F L O W ~ version 20.01.0 Launching nf-core/scrnaseq [insane_watson] - revision: 884e541285 [1.0.0] [2m---------------------------------------------------- ,--./,-. _ _ /,-..--~' |\ | | / ` / \ |) | } { | | | _, __/ | \ |__ `-.,--, .,.,' nf-core/scrnaseq v1.0.0

Pipeline Release : 1.0.0 Run Name : insane_watson Reads : data/S10_L001/_R{1,2}.fastq.gz Genome Reference : data/references/GRCm38.p6.genome.chr19/GRCm38.p6.genome.chr19.fa GTF Reference : data/references/GRCm38.p6.genome.chr19/gencode.vM19.annotation.chr19.gtf Save Reference? : false Aligner : star STARsolo Index : data/references/GRCm38.p6.genome.chr19/star/ Droplet Technology: 10x Chemistry Version : V3 Max Resources : 6.GB memory, 2 cpus, 10d time per job Container : docker - nfcore/scrnaseq:1.0.0

Shouldn't 'makeSTARindex' be switched off when using a star_index?

Best, Momo

[apeltzer]

It should - I fear I have to really sit down with this pipeline a couple of times more to fix some of the issues we have. Currently quite swamped with other things unfortunately, so if someone wants to have a go :-)

[tthyer]

+1 I also encountered this error

[joefranchesco]

I'm also running into this.

[chaochungkuo]

Same here.

[apeltzer]

The DSLv2 rewrite is almost ready -- please have a look at the dsl2 branch of this pipeline that should cover a large portion of the pipeline updates and also ffix this 👍🏻

[apeltzer]

Fixed in dev