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License: MIT License
An RNASeq pipeline
License: MIT License
repeated arg in collectrnaseqmatrics rule fail the pipeline
${arg}
need to comment this line ##### # STRAND=SECOND_READ_TRANSCRIPTION_STRAND
Line No. 379
See #9
multiqc trimmgalore report collect missing
not sure why multiqc report only one sample of collectRnaSeqmatrics *RNA_Metrics.txt (AAHHT013)
Please see the results and multiqc report file here..
"/mnt/projects/rpd/devs/justin/rpd-rnaseq-test/results/MultiQC/multiqc_report.html"
repeated arg in collectrnaseqmatrics rule fail the pipeline
${arg}
need to comment this line ##### # STRAND=SECOND_READ_TRANSCRIPTION_STRAND
Line No. 379
3.
Linne No. 388
change rseqc results outside the sample_id folder.
Leave note on how to use publishdir and workdir (and how to cleanup) in docs
Linne No. 388
change rseqc results outside the sample_id folder.
See #9
No sample based folder per analysis
push all the samples published results to relevant folders
bigwig/
_fwd.bw
_rev.bw
RnaSeqMetrics/
_RNA_Metrics.txt
rsem/
.genes.results
.isoforms.results
.pdf
.stat
rseqc/
plot.pdf
dup_pos/.pos.DupRate.xls
dup_seq/seq.DupRate.xls
rscripts/plot.r
read_distribution/.read_distribution.txt
bam_stat/.bam_stat.txt
STAR/
bam/_Aligned.sortedByCoord.out.bam
bam/_Aligned.toTranscriptome.out.bam
count/_ReadsPerGene.out.tab
logs/Log.final.out
logs/SJ.out.tab
logs/Log.progress.out
move fastqc to out/ folder
move MultiQC to out/ folder
keep the
remove the following under "Library strandedness "
(Reference format https://github.com/nf-core/rnaseq/blob/master/docs/usage.md)
"""
Specifying --pico makes the pipeline run in forward_stranded mode.
You can set a default in a custom Nextflow configuration file such as one saved in ~/.nextflow/config (see the nextflow docs for more). For example:
params {
reverse_stranded = true
}
If you have a default strandedness set in your personal config file you can use --unstranded to overwrite it for a given run."
""""
Include the below..
"""
These flags affect the commands used for several steps in the pipeline - namely RSEM and picard collectRnaSeqMetrics
:
RSEM:
--unstranded none
--forward_stranded forward
--reverse_stranded reverse (Illumina TruSeq Stranded protocols)
Picard collectRnaSeqMetrics:
--unstranded STRAND_SPECIFICITY=NONE
--forward_stranded || singleend STRAND_SPECIFICITY=FIRST_READ_TRANSCRIPTION_STRAND
--reverse_stranded STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND
""""
not sure why multiqc report only one sample of collectRnaSeqmatrics *RNA_Metrics.txt (AAHHT013)
Please see the results and multiqc report file here..
"/mnt/projects/rpd/devs/justin/rpd-rnaseq-test/results/MultiQC/multiqc_report.html"
See #9
esp. remove CPU settings for programs not using them or adjust for those not using them efficiently (FastQC, MultiQC, Picard)
fastqc html and zip files were not written in the publish dir
/mnt/projects/rpd/devs/justin/rpd-rnaseq-test/results/fastqc
Logging activity needs to bemonitored
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