Hi, I see the big changes about this workflow, and I want to download the new pipeline to run. And I use the command

nohup nextflow run nf-core/circrna -r dev -profile test &

,but it always stopped. From the .nextflow.log, I do not see the error message, and it does not start the analysis. I know the pipeline that I am running is not the latest, and the version is 'vdev-gc29124f' . So,I tried to pull the latest version using

nohup nextflow pull nf-core/circrna > download.log

,and it failed,too. The download.log says "nf-core/circrna contains uncommitted changes -- cannot pull from repository" .So,how can I run the new pipeline. using

git clone <https://github.com/nf-core/circrna.git>

? Thanks for your answers! `Jun-21 115730.079 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation Jun-21 115731.685 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: 'input': '/nf-core/test-datasets/circrna/sa mples.csv' with '/home/guozw/.nextflow/assets/nf-core/circrna/assets/schema_input.json' Jun-21 115741.925 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: 'input': '/nf-core/test-datasets/circrna/samp les.csv' with '/home/guozw/.nextflow/assets/nf-core/circrna/assets/schema_input.json' Jun-21 115741.926 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation Jun-21 115741.931 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: '/nf-core/test-datasets/circrna/samples.csv ' with '/home/guozw/.nextflow/assets/nf-core/circrna/assets/schema_input.json' Jun-21 115747.504 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: '/nf-core/test-datasets/circrna/samples.csv' with '/home/guozw/.nextflow/assets/nf-core/circrna/assets/schema_input.json' Jun-21 115747.771 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: '/nf-core/test-datasets/circrna/samples.csv ' with '/home/guozw/.nextflow/assets/nf-core/circrna/assets/schema_input.json' Jun-21 115753.655 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: '/nf-core/test-datasets/circrna/samples.csv' with '/home/guozw/.nextflow/assets/nf-core/circrna/assets/schema_input.json' Jun-21 115755.645 [main] DEBUG nextflow.script.ProcessConfig - Config settings

withLabel:process_single

matches labels

process_sin
gle

for process with name NFCORE_CIRCRNACIRCRNACAT_FASTQ Jun-21 115755.650 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-21 115755.650 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-21 115755.654 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Jun-21 115755.658 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=64; memory=2 51 GB; capacity=64; pollInterval=100ms; dumpInterval=5m Jun-21 115755.660 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) Jun-21 115755.715 [main] DEBUG nextflow.script.ProcessConfig - Config settings

withLabel:process_medium

matches labels

process_med
ium

for process with name NFCORE_CIRCRNACIRCRNAPREPARE_GENOME:SEQKIT_SPLIT Jun-21 115755.715 [main] DEBUG nextflow.script.ProcessConfig - Config settings

withName:SEQKIT_SPLIT

matches process NFCORE_CIRCRNA CIRCRNAPREPARE_GENOME:SEQKIT_SPLIT Jun-21 115755.717 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-21 115755.717 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-21 115755.722 [main] DEBUG nextflow.script.ProcessConfig - Config settings

withLabel:process_high

matches labels

process_high

for process with name NFCORE_CIRCRNACIRCRNAPREPARE_GENOME:BOWTIE_BUILD Jun-21 115755.747 [main] DEBUG nextflow.script.ProcessConfig - Config settings

withName:HISAT2_BUILD

matches process NFCORE_CIRCRNACIRCRNAPREPARE_GENOME:HISAT2_BUILD Jun-21 115755.749 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-21 115755.749 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-21 115755.757 [main] DEBUG nextflow.script.ProcessConfig - Config settings

withLabel:process_high

matches labels

process_high

for process with name NFCORE_CIRCRNACIRCRNAPREPARE_GENOME:STAR_GENOMEGENERATE Jun-21 115755.758 [main] DEBUG nextflow.script.ProcessConfig - Config settings

withName:STAR_GENOMEGENERATE

matches process NFCORE_CIRCRNACIRCRNAPREPARE_GENOME:STAR_GENOMEGENERATE Jun-21 115755.760 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-21 115755.760 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-21 115755.767 [main] DEBUG nextflow.script.ProcessConfig - Config settings

withLabel:process_high

matches labels

process_high

for process with name NFCORE_CIRCRNACIRCRNAPREPARE_GENOME:SEGEMEHL_INDEX Jun-21 115755.767 [main] DEBUG nextflow.script.ProcessConfig - Config settings

withName:SEGEMEHL_INDEX

matches process NFCORE_CIRCRNACIRCRNAPREPARE_GENOME:SEGEMEHL_INDEX Jun-21 115755.768 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-21 115755.768 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' `

Hey, I also don't know why the run terminates without any message. Maybe you should try running without the

&

just to make sure that you see everything that would be printed to the terminal also. For pipeline update, it looks like there are uncommitted changes in your local clone. The clone should be located in

~/.nextflow/assets/nf-core

. If you know what you are doing you can try to remove these changes manually, otherwise just delete the directory and use the automatic cloning again.

Thanks, like you said, I really made some changes in the download version code. In order to use the latest version, I just remove the directory, and use the

nextflow run nf-core/circrna -r dev -profile test,conda

to let it download again. And that works. thanks a lot!! Another question that I meet is that: Although it does not recommend using the profile conda, but because of the reality, the cluster that I used only has conda, I have to use that. And there is always a question about making new conda env about the pandas. In reality, the version of pandas=1.5.2 can not find in the bioconda, so, it always fails. conda-forge has this. Could you fix this ? ERROR ~ Error executing process > 'NFCORE_CIRCRNACIRCRNACIRCRNA_DISCOVERY:MERGE_SAMPLES' Caused by: Failed to create Conda environment command: conda create --mkdir --yes --quiet --prefix /home/guozw/hant/project/Test_circRNA_nf_0621/work/conda/env-d10ce34b5df8083f57a3a4a57642b6e6 -c conda-forge -c bioconda -c defaults bioconda::pandas=1.5.2 status : 1 message: Channels: - conda-forge - bioconda - defaults Platform: linux-64 Collecting package metadata (repodata.json): ...working... Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError("<urllib3.connection.HTTPSConnection object at 0x7f26ade85dc0>: Failed to resolve 'repo.anaconda.com' ([Errno -2] Name or service not known)")': /pkgs/r/linux-64/repodata.json.zst done Solving environment: ...working... failed PackagesNotFoundError: The following packages are not available from current channels: - bioconda::pandas==1.5.2 Current channels: - https://conda.anaconda.org/conda-forge - https://conda.anaconda.org/bioconda - defaults - https://conda.anaconda.org/bioconda

Conda is not really well-tested with this pipeline, so you might stumble over a few more problems like this. However, they should not be too hard to fix - I am currently commuting but I can do it in an hour or so Alternatively, you could try to make the changes locally and create a PR from there 😉

Hi, about the last question: I know it does not recommend using the profile conda, but because of the reality, I have to use conda. So, I hope you can fix it. And about this mistakes "bioconda::pandas==1.5.2" . I have seen several times in the main.nf. Because of the library pandas is widely used. I hope you can fix it.😁 If you decide to fix the problems about conda, there is another : in the local modules. for example, quantification/split_types/main.nf

conda "${moduleDir}/environment.yml"

,but I cannot find the file. like that quantification<//main.nf|/transcriptome /main.nf> , tximeta/tximeta/main.nf , they do not have this file.😔 I tried to use the singularity. And there is also a question about the enviroment : And I search the url 'https://depot.galaxyproject.org/singularity/biocontainers/r-base:4.2.1', it shows 404. """ Pulling Singularity image https://depot.galaxyproject.org/singularity/bioconductor-rtracklayer:1.62.0--r43ha9d7317_0 [cache /home/guozw/nextflow/circrna/depot.galaxyproject.org-singularity-bioconductor-rtracklayer-1.62.0--r43ha9d7317_0.img] Pulling Singularity image https://depot.galaxyproject.org/singularity/biocontainers/r-base:4.2.1 [cache /home/guozw/nextflow/circrna/depot.galaxyproject.org-singularity-biocontainers-r-base-4.2.1.img] ERROR ~ Error executing process > 'NFCORE_CIRCRNACIRCRNASTATISTICAL_TESTS:CIRCTEST_PREPARE' Caused by: Failed to pull singularity image command: singularity pull --name depot.galaxyproject.org-singularity-biocontainers-r-base-4.2.1.img.pulling.1719021591622 https://depot.galaxyproject.org/singularity/biocontainers/r-base:4.2.1 > /dev/null status : 255 message: INFO: Downloading network image FATAL: the requested image was not found -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details "" I was sorry for causing you so many problems. 🤣

Thanks for pointing this out - will look into it later today

I do not know how to use this branch. so, I just use the chatGPT, using the command

git fetch origin

git checkout -b conda-envs origin/conda-envs

git branch

, and I see I am on the conda-envs branch. But I do not know what to do next?? I just run the command like before

nextflow run nf-core/circrna -profile test,conda -r dev -bg

,but it also failed on the conda env . I think maybe there is something about using the conda-envs. ERROR ~ Error executing process > 'NFCORE_CIRCRNACIRCRNACIRCRNA_DISCOVERY:MERGE_TOOLS (5)' Caused by: Failed to create Conda environment command: conda create --mkdir --yes --quiet --prefix /home/guozw/hant/project/Test_circRNA_nf_0621/work/conda/env-d10ce34b5df8083f57a3a4a57642b6e6 -c conda-forge -c bioconda -c defaults bioconda::pandas=1.5.2 status : 1 message: Channels: - conda-forge - bioconda - defaults Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed PackagesNotFoundError: The following packages are not available from current channels: - bioconda::pandas==1.5.2

Yes, I thought you knew because you already specify the branch using "-r dev". Just replace "dev" with the new branch name

NFCORE_CIRCRNACIRCRNAQUANTIFICATION:TXIMETA_TXIMETA .

modules/local/tximeta/tximeta/environment.yml

The file does not exists. Please help to fix that.

Done - please pull again

NFCORE_CIRCRNACIRCRNAQUANTIFICATION:MERGE_EXPERIMENTS

modules/local/quantification/merge_experiments/environment.yaml

The file does not exists. Please help to fix that. 😂

How do I always miss one more xD

It failed,....😔 This time I can not see the error message. bioconda::bioconductor-rtracklayer==1.62.0--r43ha9d7317_0 is right from I see in my mamba search. ERROR ~ Error executing process > 'NFCORE_CIRCRNACIRCRNAQUANTIFICATION:MERGE_EXPERIMENTS' Caused by: Failed to create Conda environment command: conda env create --prefix /home/guozw/hant/project/Test_circRNA_nf_0621/work/conda/fishpond_swish-fbfb4f71afddbe4a54caf58a5a536aae --file /home/guozw/.nextflow/assets/nf-core/circrna/./workflows/circrna/../../subworkflows/local/../../modules/local/quantification/merge_experiments/environment.yml status : 1 message: CondaValueError: invalid package specification: bioconda::bioconductor-rtracklayer==1.62.0--r43ha9d7317_0

Please give it another try now

Thanks for your help!! I successfully complete the pipeline!! 🥰

Ok great - then I will create a PR and merge the branch into

dev

soon