update pipeline: flexiplex cannot output gz file

mritchielab · Jul 21, 2023 · 61f8c42 · 61f8c42
1 parent cb526a7
commit 61f8c42
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/R/sc_long_multisample_pipeline.R b/R/sc_long_multisample_pipeline.R
@@ -137,7 +137,7 @@ sc_long_multisample_pipeline <-
  if (length(barcodes_file) != length(fastqs)) {
  stop(length(barcodes_file), " barcode allow-lists provided while there are ", length(fastqs), "fastq file. Please either provide one allow-list per sample, or one allow-list for all samples.")
  }
- infqs <- file.path(outdir, paste(samples, "matched_reads.fastq.gz", sep = "_"))
+ infqs <- file.path(outdir, paste(samples, "matched_reads.fastq", sep = "_"))
  bc_stats <- file.path(outdir, paste(samples, "matched_barcode_stat", sep = "_"))
  for (i in 1:length(fastqs)) {
  find_barcode(

diff --git a/R/sc_long_pipeline.R b/R/sc_long_pipeline.R
@@ -125,7 +125,7 @@ sc_long_pipeline <-
  if (!file.exists(barcodes_file)) {
  stop("barcodes_file must exists.")
  }
- infq <- file.path(outdir, "matched_reads.fastq.gz")
+ infq <- file.path(outdir, "matched_reads.fastq")
  bc_stat <- file.path(outdir, "matched_barcode_stat")
  find_barcode(
  fastq = fastq,