Documentation ommission: nextflow workflow locations

[pvanheus]

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.