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pipecraft's Introduction

PipeCraft2

Release 1.0.0

Download: https://github.com/pipecraft2/pipecraft/releases/tag/v1.0.0

USER GUIDE: https://pipecraft2-manual.rtfd.io

For developers

Dockerhub: https://hub.docker.com/u/pipecraft

Prerequisites:

NodeJS https://nodejs.org/en/download/ (make sure you lets node install build tools on windows and build-essential on ubuntu) Yarn (https://classic.yarnpkg.com/en/docs/install/#windows-stable)
Docker: windows(https://www.docker.com/get-started) ubuntu and based distros bash curl -fsSL https://get.docker.com -o get-docker.sh sudo sh get-docker.sh https://docs.docker.com/engine/install/linux-postinstall/
Git (https://git-scm.com/downloads)

git clone https://github.com/pipecraft2/pipecraft
cd pipecraft
yarn run install_pipe
yarn electron:serve

pipecraft's People

Contributors

anslan avatar dependabot[bot] avatar mets0ja avatar vmikk avatar

Watchers

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Forkers

mets0ja

pipecraft's Issues

pipecraft/pandaseq:2.11

Hi,

I am using the workflow (https://dockstore.org/workflows/github.com/ShalekLab/ampliconBCR/ampliconBCR_solo:main?tab=info) and ultimately i am having an issue when running a pipeline.

The panda_express task in the workflow calls the pipecraft/pandaseq:2.11 docker it's run time. This is the task that is having the error (PAPI error code7) when it's run. The container doesn't appear in searches in Docker Hub.

Can you please rehost the image or hand over the Dockerfile you were using? That would be extremely helpful.

Thank you a lot.
Faez

LULU postclustering step error

Hi,

When running LULU in pipecraft2, pipecraft stops and reports 'ERROR]:' without any additional information. When I look at the R_run.log in the lulu_out output folder it says:

Error in library(devtools) : there is no package called 'devtools' Execution halted

Can I install devtools myself, or does the pipecraft LULU docker image needs to be updated (fyi I'm using Pipecraft_v0.1.4)?

Kind regards,
Sam

demultiplexing - not all indexes unique

Index fasta file for demultiplexing produces an error when using mixed end of line styles: \r \n
Issue resolved by using windows-style at every line end.

Pipecraft v.1.0.0 NextITS workflow does not work: There's no process matching config selector

Hi,

When trying the Pipecraft v.1.0.0 NextITS workflow I get the following error messages:

N E X T F L O W  ~  version 23.04.1
Launching `/scripts/NextITS/Step2_AggregateRuns.nf` [admiring_golick] DSL2 - revision: e9da2772b3
WARN: There's no process matching config selector: qc_se
WARN: There's no process matching config selector: qc_pe
WARN: There's no process matching config selector: disambiguate
WARN: There's no process matching config selector: demux
WARN: There's no process matching config selector: demux_illumina
WARN: There's no process matching config selector: demux_illumina_notmerged
WARN: There's no process matching config selector: merge_pe
WARN: There's no process matching config selector: prep_barcodes
WARN: There's no process matching config selector: primer_check
WARN: There's no process matching config selector: itsx
WARN: There's no process matching config selector: seq_qual
WARN: There's no process matching config selector: homopolymer
WARN: There's no process matching config selector: chimera_ref
WARN: There's no process matching config selector: chimera_rescue
WARN: There's no process matching config selector: chimera_denovo
WARN: There's no process matching config selector: chimera_denovo_agg
WARN: There's no process matching config selector: glob_derep
WARN: There's no process matching config selector: pool_seqs
WARN: There's no process matching config selector: otu_clust
WARN: There's no process matching config selector: otu_tab
WARN: There's no process matching config selector: tj
WARN: There's no process matching config selector: prep_seqtab
WARN: There's no process matching config selector: read_counts
WARN: There's no process matching config selector: quick_stats
ERROR ~ No files match pattern `**/07_SeqTable/Seqs.RData` at path: /input/Step1_Results/

 -- Check '.nextflow.log' file for details
ERROR ~ No files match pattern `**/07_SeqTable/Seqs.fa.gz` at path: /input/Step1_Results/

 -- Check '.nextflow.log' file for details
Pipeline execution stopped with the following message: No files match pattern `**/07_SeqTable/Seqs.fa.gz` at path: /input/Step1_Results/
Pipeline execution stopped with the following message: No files match pattern `**/07_SeqTable/Seqs.fa.gz` at path: /input/Step1_Results/
Pipeline completed at : 2023-11-06T11:23:16.190297Z
Duration              : 1.3s
Execution status      : Failed

It seems like Pipecraft does not recognize the processes that are defined in the full Pipecraft NextITS workflow, it runs like no processes or tools have been selected?

In any case, I selected my work directory containing demultiplexed PacBio ITS (single-end) amplicons (which have been demultiplexed using the previous version of pipecraft2 (v.0.1.4) using the SELECT WORKDIR button, after which I selected the NextITS pipeline using the SELECT PIPELINE button in the top left corner. I only edited the reverse primer because it was missing the first two bases, and selected the UNITE_9_1_beta.fasta file as the chimera database for reference based chimera filtering. Other than that I did not change any of the other default parameters.

Mac installation error

Hello,

I have tried to install the .pkg file on two seperate intel macs. One double clicking the icon a message appears saying "pipecraft can't be installed on this computer".

That's as far as I can get....

Screenshot 2023-10-10 at 5 48 17 PM

Run Workflow Missing selected services or mandatory inputs

Hi,

I have selected my working directory which contains one fastq.gz file (after selecting multiplexed / fastq.gz / single end, as file type), added a demultiplex step, and uploaded my index fasta file, which looks like this:

>Molenbeek_0_10
AGACAACTC...CGTCCTA
>Herentals_0_10
TTCGGCATT...ATATCGA
>Diepenbeek_0_10
GAATCTAAC...GCGGAGT
>Burdinne_0_10
TTCGAACCT...TCCGAGC
>Cerfontaine_0_10
GAACCAATC...GAACCAATC

However, when I try to run the workflow, it says 'Missing selected services or mandatory inputs' (and the button is red)

Quality check however worked fine

Any idea what I am missing here?

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