Salmon expanded

.gitignore

@@ -2,5 +2,7 @@ nextflow
 .nextflow
 .nextflow.*
 pipeline_trace*
-nf_pipeline
-work
+nf_pipeline*
+work
+*.fa
+*.gtf

cleanup.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+./nextflow main.nf -profile test
+rm -rf work
+rm -rf nf_pipeline
+rm .nextflow.log*
+rm pipeline_trace.txt*

conda.yml

@@ -6,7 +6,7 @@ channels:
   - conda-forge
 dependencies:
   # Default bismark
-  - salmon
-  - alevin-fry
-  - pyroe
+  - bioconda::salmon>=1.8.0
+  - bioconda::alevin-fry>=0.6.0
+  - bioconda::pyroe
   - bedtools

input_files/pl_sheet_toy.tsv

@@ -1,2 +1,2 @@
-reference	link
+chemistry	link
 v3	https://raw.githubusercontent.com/10XGenomics/cellranger/master/lib/python/cellranger/barcodes/3M-february-2018.txt.gz

input_files/ref_sheet.tsv

@@ -1,3 +1,3 @@
 reference	link
 human2020A	https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz
-mm10-2020A	https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz
+mm10-2020A	https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz

input_files/ref_sheet_toy.tsv

@@ -1,2 +1,2 @@
-reference	link
-human-toy	https://umd.box.com/shared/static/7v6mof9emgudmuczc4lnwz4oou7xayks.gz
+reference	ref_data	fasta	gtf
+human-toy-download-ref	randommeaninglessfillerstring	genomic_data/fasta/genome.fa	genomic_data/genes/genes.gtf

input_files/sample_sheet_toy.tsv

@@ -1,2 +1,2 @@
 chemistry	reference	dataset_name	dataset_url	fastq_url	fastq_MD5sum	delete_fastq	feature_barcode_csv_url	multiplexing_library_csv_url
-v3	human-toy	toy set from 200 Sorted Cells from Human Glioblastoma Multiforme, 3' LT v3.1	https://www.10xgenomics.com/resources/datasets/200-sorted-cells-from-human-glioblastoma-multiforme-3-lt-v-3-1-3-1-low-6-0-0	https://umd.box.com/shared/static/bauvay4eq0v8xmu9e0fp0me7zj1qojnr.tar	8db8f1f92f92de0295efc9bb602a8276	1		
+v3	human-toy-download-ref	toy set from 200 Sorted Cells from Human Glioblastoma Multiforme, 3' LT v3.1	https://www.10xgenomics.com/resources/datasets/200-sorted-cells-from-human-glioblastoma-multiforme-3-lt-v-3-1-3-1-low-6-0-0	https://umd.box.com/shared/static/bauvay4eq0v8xmu9e0fp0me7zj1qojnr.tar	8db8f1f92f92de0295efc9bb602a8276	1		

main.nf

@@ -25,7 +25,6 @@ workflow {
       // producing both the knee filtered and 
       // unfiltered output
       preprocess()
-
   // merge permit list
       data = preprocess.out.chem_pl.cross(data)
             .map(it -> tuple(it[1][1], // reference
@@ -39,7 +38,6 @@ workflow {
                               it[1][7], // feature_barcode_csv_url
                               it[1][8]  // multiplexing_library_csv_url
             ))
-
   // merge t2g and salmon index
       data = preprocess.out.ref_t2g_index.cross(data)
             .map(it -> tuple( it[1][1], // chemistry
@@ -55,7 +53,11 @@ workflow {
                               it[1][2], // pl_path
                               it[0][1] // t2g_path
             ))
-
       salmon_map(data) 
-      af(salmon_map.out, Channel.value("unfilt"))
+      if(!salmon_map.out[0].equals("v2") && !salmon_map.out[0].equals("v3")) {
+            af(salmon_map.out, Channel.value("unfilt"))
+      } else {
+            af(salmon_map.out, Channel.value("knee"))
+      }
+      af.out.view()
 }

modules/af.nf

@@ -270,6 +270,10 @@ workflow af {
         | alevin_fry_collate \
         | alevin_fry_quant \
         | write_description
+
+    emit:
+        write_description.out
+
 }