Set steps to perform in the pipeline
Examples
ppl <- example_pipeline()
#> Writing configuration parameters to: /tmp/RtmpgpEV0i/file25bf53c5338d/config_file_9663.json
#> Configured steps:
#> barcode_demultiplex: TRUE
#> genome_alignment: TRUE
#> gene_quantification: TRUE
#> isoform_identification: TRUE
#> read_realignment: TRUE
#> transcript_quantification: TRUE
#> samtools not found, will use Rsamtools package instead
steps(ppl) <- c(
barcode_demultiplex = TRUE,
genome_alignment = TRUE,
gene_quantification = TRUE,
isoform_identification = FALSE,
read_realignment = FALSE,
transcript_quantification = TRUE
)
ppl
#> → A FLAMES.SingleCellPipeline outputting to /tmp/RtmpgpEV0i/file25bf53c5338d
#>
#> ── Inputs
#> ✔ fastq: ...ibrary/FLAMES/extdata/fastq/musc_rps24.fastq.gz
#> ✔ annotation: /__w/_temp/Library/FLAMES/extdata/rps24.gtf.gz
#> ✔ genome_fa: /tmp/RtmpgpEV0i/file25bf53c5338d/rps24.fa
#> ✔ barcodes_file: /tmp/RtmpgpEV0i/file25bf53c5338d/bc_allow.tsv
#>
#> ── Outputs
#> ℹ demultiplexed_fastq: matched_reads.fastq
#> ℹ deduped_fastq: matched_reads_dedup.fastq
#> ℹ genome_bam: align2genome.bam
#> ℹ transcriptome_assembly: transcript_assembly.fa
#> ℹ transcriptome_bam: realign2transcript.bam
#>
#> ── Pipeline Steps
#> ℹ barcode_demultiplex (pending)
#> ℹ genome_alignment (pending)
#> ℹ gene_quantification (pending)
#> ℹ transcript_quantification (pending)
# or partially change a step:
steps(ppl)["read_realignment"] <- TRUE
ppl
#> → A FLAMES.SingleCellPipeline outputting to /tmp/RtmpgpEV0i/file25bf53c5338d
#>
#> ── Inputs
#> ✔ fastq: ...ibrary/FLAMES/extdata/fastq/musc_rps24.fastq.gz
#> ✔ annotation: /__w/_temp/Library/FLAMES/extdata/rps24.gtf.gz
#> ✔ genome_fa: /tmp/RtmpgpEV0i/file25bf53c5338d/rps24.fa
#> ✔ barcodes_file: /tmp/RtmpgpEV0i/file25bf53c5338d/bc_allow.tsv
#>
#> ── Outputs
#> ℹ demultiplexed_fastq: matched_reads.fastq
#> ℹ deduped_fastq: matched_reads_dedup.fastq
#> ℹ genome_bam: align2genome.bam
#> ℹ transcriptome_assembly: transcript_assembly.fa
#> ℹ transcriptome_bam: realign2transcript.bam
#>
#> ── Pipeline Steps
#> ℹ barcode_demultiplex (pending)
#> ℹ genome_alignment (pending)
#> ℹ gene_quantification (pending)
#> ℹ read_realignment (pending)
#> ℹ transcript_quantification (pending)