nf-core/cageseq

CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

cageseq's Issues

Into causing error line 130 of main.nf

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

error: make_ctss.sh: line 18: Read-only file system Read-only file system

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

My attempts at fixes that haven't worked

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.

Where are the versions numbers stored?

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."

Add alignment warnings for bowtie

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.

release first version

Features:

• fastqc
• trimming
• trimming fastqc
• mapping
• mapping qc
• clustering cage tags
• clustering qc

Documentation:

• output.md
• usage.md
• [ ]

Missing branch: dev and TEMPLATE

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.

cageseq error

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-