From 61f8c426057cc28d115d4ff7d512487601da6549 Mon Sep 17 00:00:00 2001 From: Changqing Wang Date: Fri, 21 Jul 2023 17:06:30 +1000 Subject: [PATCH] update pipeline: flexiplex cannot output gz file --- R/sc_long_multisample_pipeline.R | 2 +- R/sc_long_pipeline.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/sc_long_multisample_pipeline.R b/R/sc_long_multisample_pipeline.R index 569ed91..2852f4f 100755 --- 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 index 0c6afd6..07284a5 100755 --- 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,