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View Code? Open in Web Editor NEWCAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
Home Page: https://nf-co.re/cageseq
License: MIT License
CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
Home Page: https://nf-co.re/cageseq
License: MIT License
Operator into
has been deprecated -- it's not available in DSL2 syntax
-- Check script '/rhome/aboyd003/.nextflow/assets/nf-core/cageseq/main.nf' at line: 130
Hi,
I don't know if this technically qualifies as a bug but I am having issue using the pipeline on a hpcc. I don't have sudo privileges and am using singularity. I receive the error below when running with the test file (nextflow run nf-core/cageseq -r 1.0.2 -dsl1 -profile test,singularity).
make_ctss.sh: line 18: /tmp/make_ctss.sh.17128.txt: Read-only file system
I have tried inserting a binding line into the Dockerfile at line 11 after the ENV PATH line. This seemed the most logical to me. I tried "exec --bind /scratch:/tmp" and "export SINGULARITY_BINDPATH=/scratch:/tmp" at this position. When this failed, I tried inserting the lines into line 12 of main.nf. I honestly did not expect this to work but figured I would try. I also tried inserting in the singularity block of nextflow.config at line 111.
The link in the text below redirects to an empty page?
"First, go to the nf-core/cageseq releases page and find the latest version number - numeric only (eg. 1.3.1). Then specify this when running the pipeline with -r (one hyphen) - eg. -r 1.3.1."
Currently warnings for failed or low-percentage alignments are only implemented for the star alignment process.
Would be nice if we can implement this for bowtie as well.
Features:
Documentation:
Hi,
I'm looking at all pipelines, and I noticed that this one is missing some branches.
All pipelines should have a dev
branch and a TEMPLATE
branch.
Hi
I am getting input tuple error. Could you please help me with this?
WARN: Access to undefined parameter `config_profile_contact` -- Initialise it to a default value eg. `params.config_profile_contact = some_value`
WARN: Access to undefined parameter `config_profile_url` -- Initialise it to a default value eg. `params.config_profile_url = some_value`
Run Name : big_payne
Input : sample_1/*R1.fastq.gz
5' artifacts : software/cageseq/assests/artifacts_5end.fasta
3' artifacts : software/cageseq/assests/artifacts_3end.fasta
trim_ecop : true
trim_linker : true
trim_5g : true
trim_artifacts : true
eco_site : CAGCAG
linker_seq : TCGTATGCCGTCTTC
Remove rRNA : true
Aligner : STAR
STAR Index : hg38.analysisSet.chroms
Min. cluster : 30
Cluster Threshold : 0.2
bigwig output : Yes
Save Reference : false
Max Resources : 160 GB memory, 20 cpus, 5d 23h time per job
Output dir : test_results/
Launch dir : software
Working dir : software/work
Script dir : software/cageseq
User : KG
Config Profile : chimera
Config Files : software/cageseq/nextflow.config
----------------------------------------------------
No signature of method: java.lang.Boolean.getFileSystem() is applicable for argument types: () values: []
WARN: Input tuple does not match input set cardinality declared by process `fastqc` -- offending value: sample_1/sample.R1.fastq.gz
WARN: Input tuple does not match input set cardinality declared by process `trim_adapters` -- offending value: sample_1/sample.R1.fastq.gz
[- ] process > get_software_versions -
[- ] process > convert_gtf -
-[nf-core/cageseq] Pipeline completed with errors-
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