cores	8
ram	30
scratch	100
partition	user
process_mode	DATASET
samples	S1_undiff,S2_undiff,S3_undiff,S4_diff,S5_diff,S6_diff
nfcorePipeline	rnaseq
pipelineVersion	3.19.0
inputType	samplesheet
samplesheetMapping	"{""sample"":""Name"",""fastq_1"":""Read1 [File]"",""fastq_2"":""Read2 [File]"",""strandedness"":""StrandMode""}"
pseudo_aligner	""
skip_alignment	""
multiqc_title	""
genome	""
fasta	""
gtf	""
gff	""
gene_bed	""
transcript_fasta	""
additional_fasta	""
splicesites	""
star_index	""
hisat2_index	""
rsem_index	""
salmon_index	""
kallisto_index	""
hisat2_build_memory	200.GB
gencode	false
gtf_extra_attributes	gene_name
gtf_group_features	gene_id
featurecounts_group_type	gene_biotype
featurecounts_feature_type	exon
trimmer	trimgalore
extra_trimgalore_args	""
extra_fastp_args	""
min_trimmed_reads	10000
bbsplit_fasta_list	""
bbsplit_index	""
sortmerna_index	""
remove_ribo_rna	false
ribo_database_manifest	${projectDir}/workflows/rnaseq/assets/rrna-db-defaults.txt
with_umi	false
umi_dedup_tool	umitools
umitools_extract_method	string
umitools_bc_pattern	""
umitools_bc_pattern2	""
umi_discard_read	0
umitools_umi_separator	""
umitools_grouping_method	unique
umitools_dedup_stats	false
aligner	star_salmon
pseudo_aligner_kmer_size	31
bam_csi_index	false
star_ignore_sjdbgtf	false
salmon_quant_libtype	A
min_mapped_reads	5
seq_center	""
stringtie_ignore_gtf	false
extra_star_align_args	""
extra_salmon_quant_args	""
extra_kallisto_quant_args	""
kallisto_quant_fraglen	200
kallisto_quant_fraglen_sd	200
stranded_threshold	0.8
unstranded_threshold	0.1
save_merged_fastq	false
save_umi_intermeds	false
save_non_ribo_reads	false
save_bbsplit_reads	false
save_reference	false
save_trimmed	false
save_align_intermeds	false
save_unaligned	false
save_kraken_assignments	false
save_kraken_unassigned	false
extra_fqlint_args	--disable-validator P001
deseq2_vst	true
rseqc_modules	bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication
contaminant_screening	kraken2
kraken_db	""
bracken_precision	D
skip_gtf_filter	false
skip_gtf_transcript_filter	false
skip_bbsplit	true
skip_umi_extract	false
skip_linting	false
skip_trimming	false
skip_pseudo_alignment	false
skip_markduplicates	false
skip_bigwig	false
skip_stringtie	false
skip_fastqc	false
skip_preseq	true
skip_dupradar	false
skip_qualimap	false
skip_rseqc	false
skip_biotype_qc	false
skip_deseq2_qc	false
skip_multiqc	false
skip_qc	false
sushi_app	NfCoreRnaseqApp
refBuild	Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03