nf-core / lncpipe Goto Github PK

Hi, Dr. Zhao,

I try to install Dependencies for LncPipe. But when I install CPAT:Citation. There is a command mv dat/* /LncPipeDB/. Where should LncPipeDB be? There is no such folder in LncPipe. Should it be created as /root/LncPipeDB/?

Thank you so much!

Best,
Yu

Actually, there are just two tools missing:

• https://sourceforge.net/projects/plek/

• LncPipeReporter

• PLEK https://ncu.dl.sourceforge.net/project/plek/PLEK.1.2.tar.gz

• LncPipeReporter（via GitHub) RUN Rscript -e "source('http://bioconductor.org/biocLite.R'); install.packages(c('curl', 'httr')); install.packages('devtools'); devtools::install_github('bioinformatist/LncPipeReporter')"

Shouldn't be too difficult to get these to bioconda and then reference them in the Dockerfile.

Can you please keep the template branch ? Pipeline syncing is coming soon and having that from the start would be easier for syncing later

NB: The logo in the readme has been generated with the required font missing, so it's defaulted to the wrong one. Please install Maven Pro Bold (see logo requirements) and regenerate 👍

this pip run finished with :"WARN: Failed to publish file: /data/lnc_temp_file/work/39/634b45a4d025dbfd578e1a590cdc30/LncPipeReports; to: /data/lncRNA/res/Result/LncPipeReports [move] -- See log file for details"

I tried many times and do not know why

Hi @likelet,

Great to see that work is underway for this pipeline! Exciting stuff 😀 I haven't looked at the code yet (and won't until you say that it's ready for review), but the first thing that I spotted is that the name uses capitals, which is against our guidelines.

It's a little boring, but because we use multiple platforms with different naming rules (I'm looking at you, dockerhub), we decided that it's easiest if pipelines are all lower case without punctuation.

I realise that this isn't in the guidelines yet so I'll add it. The new creating pipelines documentation has some more stuff like this though and should be helpful.

Cheers,

Phil

Hi,

I am having trouble running LncPipe for single-end RNA-seq data.

Here is the error message:

Caused by:
  Missing output file(s) `*qc.fq.gz` expected by process `Run_FastP (samplename)`

Command executed:

  fastp -i samplename.fastq.gz -o samplename.qc.gz -h samplename_fastp.html

It seems like the output file from the previous step is named ending with "*.qc.gz", but the process Run_FastP (samplename) looks for files ending with "*qc.fq.gz".

Is it because of this line of code in the main.nf ?

if (params.singleEnd) {
                '''
            fastp -i !{fastq_file[0]} -o !{samplename}.qc.gz -h !{samplename}_fastp.html
           
            '''
            } else {
                '''
            fastp -i !{fastq_file[0]}  -I !{fastq_file[1]} -o !{samplename}_1.qc.fq.gz  -O !{samplename}_2.qc.fq.gz -h !{samplename}_fastp.html
            '''
            }
        }
    }else{
        Channel.fromFilePairs(reads, size: params.singleEnd ? 1 : 2)

Please help!

Thanks,
Manci

Please use a dev branch as well! Master is later for stable releases and its okay to develop in it atm when polishing/updating the pipeline to a functional state but keep it in mind :-)

Hello,

When I run this command :

singularity pull --name nf-core-lncpipe.simg shub://nf-core/lncpipe

I got this:
FATAL: While pulling shub image: failed to get manifest for: shub://nf-core/lncpipe: the requested manifest was not found in singularity hub

Is there another way to pull the image ?

Thank you.

Hello!
I'm trying to run the pipeline and this error appears all the time...
I alredy tried a lot of things, even running a older version of the code, but this error appears ever...
Can anyone help me please?

blur@epi_lab:~$ sudo nextflow run nf-core/lncpipe -profile docker
N E X T F L O W  ~  version 19.01.0
Launching `nf-core/lncpipe` [chaotic_curran] - revision: 464f015763 [master]
ERROR ~ Process `Run_fastQC` is already define @ line 849, column 17.
           process Run_fastQC {
                   ^

_nf_script_3896f0c8: 875: Process `Run_afterQC` is already define @ line 875, column 17.
           process Run_afterQC {
                   ^

_nf_script_3896f0c8: 909: Process `Run_FastP` is already define @ line 909, column 17.
           process Run_FastP {
                   ^

_nf_script_3896f0c8: 1443: Process `Build_kallisto_index_of_GTF_for_quantification` is already define @ line 1443, column 17.
           process Build_kallisto_index_of_GTF_for_quantification {
                   ^

_nf_script_3896f0c8: 1460: Process `Run_kallisto_for_quantification` is already define @ line 1460, column 17.
           process Run_kallisto_for_quantification {
                   ^

_nf_script_3896f0c8: 1582: Process `Run_LncPipeReporter` is already define @ line 1582, column 17.
           process Run_LncPipeReporter {
                   ^

_nf_script_3896f0c8: 1628: Process `Run_LncPipeReporter_without_Design` is already define @ line 1628, column 17.
           process Run_LncPipeReporter_without_Design {
                   ^

7 errors


 -- Check '.nextflow.log' file for details