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Add filterScore and sjdOverhangMin parameters #136

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Jun 26, 2020
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Add filterScore and sjdOverhangMin parameters #136

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075de66
add filterScore and sjdOverhangMin
lmurba Jun 25, 2020
5b1f049
update help message to new format
lmurba Jun 25, 2020
110ab5c
update help message
lmurba Jun 25, 2020
1761f20
update usage.md
lmurba Jun 25, 2020
c4303f0
update log
lmurba Jun 25, 2020
36d18e6
update star with filterScore and sjdOverhangMin
lmurba Jun 25, 2020
7371488
Updated log indenting
PhilPalmer Jun 26, 2020
c5abd59
Updated new parameters indentation in config
PhilPalmer Jun 26, 2020
f23ce48
Updated indentation of all parameters in config
PhilPalmer Jun 26, 2020
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5 changes: 5 additions & 0 deletions docs/usage.md
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Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,11 @@ Star:
(default: 2)
--overhang Overhang (int)
(default: readlength - 1)
--filterScore Controls --outFilterScoreMinOverLread and outFilterMatchNminOverLread
(default: 0.66)
--sjdOverhangMin Controls --alignSJDBoverhangMin (int)
(default: 8)


rMATS:
--statoff Skip the statistical analysis (bool)
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92 changes: 70 additions & 22 deletions main.nf
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Expand Up @@ -20,43 +20,87 @@ def helpMessage() {
The typical command for running the pipeline is as follows:
nextflow run main.nf --reads my_reads.csv --gtf genome.gtf --star_index star_dir -profile base,sumner

Input files:
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@PhilPalmer PhilPalmer Jun 26, 2020 •
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Ah, nice idea to change the sections of input parameters in the help message & config. I much prefer your new organisation. I think it makes a lot more sense, especially as new input parameters are added for the specific tools eg STAR/trimmomatic etc.

--reads Path to reads.csv file, which specifies the sample_id and path to FASTQ files for each read or read pair (path).
This file is used if starting at beginning of pipeline.
(default: no reads.csv)
--bams Path to bams.csv file which specifies sample_id and path to BAM and BAM.bai files (path)
This file is used if starting pipeline at Stringtie.
(default: no bams.csv)
--rmats_pairs Path to rmats_pairs.txt file containing b1 (and b2) samples names (path)
(default: no rmats_pairs specified)
--download_from Database to download FASTQ/BAMs from (available = 'TCGA', 'GTEX' or 'SRA', false) (string)
(default: false)
--key_file For downloading reads, use TCGA authentication token (TCGA) or dbGAP repository key (GTEx, path)
(default: false)

Main arguments:
--reads Path to input data CSV file specifying the reads sample_id and path to FASTQ files (path)
--bams Path to input data CSV file specifying the bams sample_id and path to BAM files (path)
--gtf Path to GTF file (path)
--gtf Path to reference GTF file (path)
(default: no gtf specified)
--assembly_name Genome assembly name (available = 'GRCh38' or 'GRCm38', string)
(default: false)
--star_index Path to STAR index (path)
(default: no index specified)
--singleEnd Specifies that the input is single-end reads (bool)
(default: false)
--stranded Specifies that the input is stranded ('first-strand', 'second-strand', false (aka unstranded))
(default: 'first-strand')
--readlength Read length - Note that all reads will be cropped to this length(int)
(default: no read length specified)
-profile Configuration profile to use. Can use multiple (comma separated, string)
Available: base, docker, sumner, test and more.

Reads:
--rmats_pairs Path to file containing b1 & b2 samples names space seperated, one row for each rMATS comparison (path)
--singleEnd Specifies that the input is single-end reads (bool)
--stranded Specifies that the input is stranded (bool)
--adapter Path to adapter file (path)
--readlength Read length (int)
--overhang Overhang (default = readlength - 1, int)
--mismatch Mismatch (default = 2, int)
--minlen Drop the read if it is below a specified length (default = readlength, int)
Trimmomatic:
--minlen Drop the read if it is below a specified length (int)
Default parameters turn on --variable-readlength
To crop all reads and turn off, set minlen = readlength (NOTE: this will turn off soft clipping)
(default: 20)
--slidingwindow Perform a sliding window trimming approach (bool)

rMATS:
(default: true)
--adapter Path to adapter file (path)
(default: TruSeq3 for either PE or SE, see singleEnd parameter)

Star:
--mismatch Number of allowed mismatches per read (SE) or combined read (PE) (int)
SE ex. read length of 50, allow 2 mismatches per 50 bp
PE ex. read length of 50, allow 2 mismatches per 100 bp
(default: 2)
--overhang Overhang (int)
(default: readlength - 1)
--filterScore Controls --outFilterScoreMinOverLread and outFilterMatchNminOverLread
(default: 0.66)
--sjdOverhangMin Controls --alignSJDBoverhangMin (int)
(default: 8)

rMATS:
--statoff Skip the statistical analysis (bool)
If using only b1 as input, this must be turned on.
(default: false)
--paired_stats Use the paired stats model (bool)
--novelSS Enable detection of novel splice sites (unannotated splice sites, bool)
--mil Minimum Intron Length. Only impacts --novelSS behavior (default = 50, int)
--mel Maximum Exon Length. Only impacts --novelSS behavior (default = 500, int)
(default: false)
--novelSS Enable detection of unnanotated splice sites (bool)
(default: false)
--mil Minimum Intron Length. Only impacts --novelSS behavior (int)
(default: 50)
--mel Maximum Exon Length. Only impacts --novelSS behavior (int)
(default: 500)

Other:
--assembly_name Genome assembly name (available = 'GRCh38' or 'GRCm38', string)
--test For running QC, trimming and STAR only (bool)
--download_from Database to download FASTQ/BAMs from (available = 'TCGA', 'GTEX' or 'SRA', string)
--key_file For downloading reads, use TCGA authentication token (TCGA) or dbGAP repository key (GTEx, path)
--test For running trim test (bool)
(default: false)
--max_cpus Maximum number of CPUs (int)
(default: ?)
--max_memory Maximum memory (memory unit)
(default: 80)
--max_time Maximum time (time unit)
(default: ?)
--skiprMATS Skip rMATS (bool)
(default: false)
--skipMultiQC Skip MultiQC (bool)
(default: false)
--outdir The output directory where the results will be saved (string)
(default: directory where you submit the job)


See here for more info: https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/master/docs/usage.md
""".stripIndent()
Expand Down Expand Up @@ -103,6 +147,8 @@ log.info "rMATS novel splice sites : ${params.novelSS}"
log.info "rMATS Minimum Intron Length : ${params.mil}"
log.info "rMATS Maximum Exon Length : ${params.mel}"
log.info "Mismatch : ${params.mismatch}"
log.info "filterScore : ${params.filterScore}"
log.info "sjdOverhangMin : ${params.sjdOverhangMin}"
log.info "Test : ${params.test}"
log.info "Download from : ${params.download_from ? params.download_from : 'FASTQs directly provided'}"
log.info "Key file : ${params.key_file ? params.key_file : 'Not provided'}"
Expand Down Expand Up @@ -403,7 +449,9 @@ if (!params.bams){
--readFilesCommand zcat \
--sjdbGTFfile $gtf \
--sjdbOverhang $overhang \
--alignSJoverhangMin 8 \
--alignSJoverhangMin $params.sjdOverhangMin \
--outFilterScoreMinOverLread $params.filterScore \
--outFilterMatchNminOverLread $params.filterScore \
--outFilterMismatchNmax $params.mismatch \
--outFilterMultimapNmax 20 \
--alignMatesGapMax 1000000 \
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64 changes: 35 additions & 29 deletions nextflow.config
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Expand Up @@ -5,40 +5,46 @@ manifest {
}

params {
// Main arguments
reads = false
singleEnd = false
star_index = false
gtf = false
assembly_name = false
bams = false
// Input files
reads = false
bams = false
rmats_pairs = false
download_from = false
key_file = false

// Reads
stranded = 'first-strand'
rmats_pairs = false
adapter = false
readlength = false
overhang = false
mismatch = 2
minlen = 20
slidingwindow = true
// Main arguments:
gtf = false
assembly_name = false
star_index = false
singleEnd = false
stranded = 'first-strand'
readlength = false

// Trimmomatic:
minlen = 20
slidingwindow = true
adapter = false

// Star
overhang = false
mismatch = 2
filterScore = 0.66
sjdOverhangMin = 8

// rMATS
statoff = false
paired_stats = false
novelSS = false
mil = 50
mel = 500
statoff = false
paired_stats = false
novelSS = false
mil = 50
mel = 500

// Other
test = false
download_from = false
key_file = false
skiprMATS = false
skipMultiQC = false
outdir = 'results'
multiqc_config = "$baseDir/examples/assets/multiqc_config.yaml"
help = false
test = false
skiprMATS = false
skipMultiQC = false
outdir = 'results'
multiqc_config = "$baseDir/examples/assets/multiqc_config.yaml"
help = false
}

process {
Expand Down