Based on the example here I tried to run nextflow for the remove_contam step, but it ends with an error, as per:
$ nextflow run nextflow/remove_contam.nf -with-singularity ~/clockwork/singularity/clockwork_container.img --ref_fasta Reference.remove_contam/ref.fa --ref_metadata_tsv Reference.remove_contam/remove_contam_metadata.tsv --reads_in1 set1_1.fastq.gz --reads_in2 set1_2.fastq.gz --outprefix OUT
N E X T F L O W ~ version 19.04.1
Pulling nextflow-io/nextflow ...
Not a valid Nextflow project -- The repository `https://github.com/nextflow-io/nextflow` must contain a the script `main.nf` or the file `nextflow.config`
I discovered, upon further inspection, that this is because the assumption is that the working directory has the nextflow scripts available in the nextflow/ directory (whereas mine were elsewhere). I thought it could find the nextflow scripts in the singularity container, but this is not the case.
Perhaps this arrangement can be clarified in the Wiki.
Based on the example here I tried to run nextflow for the
remove_contamstep, but it ends with an error, as per:I discovered, upon further inspection, that this is because the assumption is that the working directory has the nextflow scripts available in the
nextflow/directory (whereas mine were elsewhere). I thought it could find the nextflow scripts in the singularity container, but this is not the case.Perhaps this arrangement can be clarified in the Wiki.