Repository may be corrupted

[wbszhu]

Hi, when i run this pipeline, the error occured:

Can't find git repository config file -- Repository may be corrupted: /public/home/luzhang/.nextflow/assets/nf-core/atacseq

Can you give me some suggestions? thanks~

[maxulysse]

If you haven't done any modification to /public/home/luzhang/.nextflow/assets/nf-core/atacseq I'd do a simple rm -rf /public/home/luzhang/.nextflow/assets/nf-core/atacseq

[wbszhu]

Hi, I try to do like you. the other error occured: https://github.com/nf-core/atacseq.git: cannot open git-upload-pack

[maxulysse]

what's your command line when running the pipeline?

[wbszhu]

Here is the command:

#module load Singularity/3.1.1
nextflow run nf-core/atacseq --input $1 -profile singularity  --fasta ~/22.genome/susScr11_xy/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa  --gtf ~/22.genome/susScr11_xy/Sus_scrofa.Sscrofa11.1.101.chr.gtf --macs_gsize 2.3e9  --bwa_min_score 25 -r 1.2.2 --outdir /public/home/luzhang/06.pig-eqtl/02.results/atac-seq/$2  -dsl1 -resume

the input file:

group,replicate,fastq_1,fastq_2
muscle,1,/public/home/luzhang/06.pig-eqtl/00.data/SRR10764667_1.fastq.gz,/public/home/luzhang/06.pig-eqtl/00.data/SRR10764667_2.fastq.gz
muscle,2,/public/home/luzhang/06.pig-eqtl/00.data/SRR10764666_1.fastq.gz,/public/home/luzhang/06.pig-eqtl/00.data/SRR10764666_2.fastq.gz

[maxulysse]

can you try:

nextflow pull nf-core/atacseq -r 1.2.2

[wbszhu]

it is also report:

nextflow pull nf-core/atacseq -r 1.2.2
Checking nf-core/atacseq ...
https://github.com/nf-core/atacseq.git: cannot open git-upload-pack

[maxulysse]

can you try:

nextflow pull hello

[wbszhu]

report like it:

nextflow pull hello
Checking hello ...
https://github.com/nextflow-io/hello.git: cannot open git-upload-pack

[maxulysse]

Can you do:

ls -l  ~/.nextflow/assets/nextflow-io/hello

and if you have something:

cd  ~/.nextflow/assets/nextflow-io/hello
git status

and copy paste the results

[wbszhu]

Cause the command "next flow pull hello" was not succeed.

ls -l ~/.nextflow/assets/nextflow-io/hello

ls: cannot access '/public/home/luzhang/.nextflow/assets/nextflow-io/hello': No such file or directory

cd ~/.nextflow/assets/nextflow-io/hello

-bash: cd: /public/home/luzhang/.nextflow/assets/nextflow-io/hello: No such file or directory

git status

fatal: Not a git repository (or any parent up to mount point /public)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

[ewels]

It sounds like there's something fishy going on with your Nextflow installation. I don't think it's related to this pipeline specifically.

I would try removing your whole Nextflow home directory (NXF_HOME env var if set, default ~/.nextflow) and trying again with the hello pipeline which is as simple as they come. If you're still having trouble, please ask for help on Slack.

Closing this issue as it's not a problem with this pipeline.