| Parameter | Value |
|---|
| 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 |
