Rnaseq: Docker Image does not seem to load

[dylanmr]

Hi,

I am trying to run the pipeline using the docker profile. However, it seems as though the pipeline is unable to load either fastqc or trim_galore. This seems to point to an issue with loading the docker image? Attached is the log file. Any help or insight is greatly appreciated.

Command:

nextflow run nf-core/rnaseq \
  -profile docker \
  --reads '/projects/dylan/criticalperiod/data/fastq/*_R{1,2}*.fastq.gz' \
  --reverse_stranded \
  --star_index '/projects/dylan/criticalperiod/data/star-GRCm38.95/genome/' \
  --fasta '/projects/dylan/criticalperiod/data/star-GRCm38.95/genome/Mus_musculus.GRCm38.cdna.all.fa' \
  --gtf '/projects/dylan/criticalperiod/data/star-GRCm38.95/Mus_musculus.GRCm38.95.gtf' \
  --outdir '/projects/dylan/criticalperiod/data/' \
  -r 1.2

Output:

Run Name       : furious_hilbert
Reads          : /projects/dylan/criticalperiod/data/fastq/*_R{1,2}*.fastq.gz
Data Type      : Paired-End
Genome         : false
Strandedness   : Reverse
Trim R1        : 0
Trim R2        : 0
Trim 3' R1     : 0
Trim 3' R2     : 0
Aligner        : STAR
STAR Index     : /projects/dylan/criticalperiod/data/star-GRCm38.95/genome/
GTF Annotation : /projects/dylan/criticalperiod/data/star-GRCm38.95/Mus_musculus.GRCm38.95.gtf
Save Reference : No
Save Trimmed   : No
Save Intermeds : No
Max Memory     : null
Max CPUs       : null
Max Time       : null
Output dir     : /projects/dylan/criticalperiod/data/
Working dir    : /nfsdata/projects/dylan/criticalperiod/code/work
Container      : [:]
Pipeline Release: 1.2
Current home   : /home/cbmr/lhv464
Current user   : lhv464
Current path   : /projects/dylan/criticalperiod/code
Script dir     : /home/cbmr/lhv464/.nextflow/assets/nf-core/rnaseq
Config Profile : docker

[apeltzer]

You might have to specify not only the -profile docker but also -profile standard,docker in releases 1.2 and earlier....

[ewels]

I think this is the solution, so will close this issue now. Feel free to reopen if it doesn't solve the issue, and would be good to know how you get on :)

Phil