add GBM example

examples/10x.GBM/run.sh

@@ -0,0 +1,26 @@
+# 10k Human PBMCs, 5' v2.0, Chromium X (with intronic reads)
+# https://www.10xgenomics.com/datasets/human-glioblastoma-multiforme-5-v-1-targeted-neuroscience-panel-1-standard-4-0-0
+mkdir 10x.GBM
+cd 10x.GBM
+
+path="https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-vdj/4.0.0/Parent_SC5v1_Human_Glioblastoma/Parent_SC5v1_Human_Glioblastoma"
+wget ${path}_possorted_genome_bam.bam -O alignment.bam
+wget ${path}_possorted_genome_bam.bam.bai -O alignment.bam.bai
+wget ${path}_analysis.tar.gz -O clusters.tar.gz
+
+# prepare input files
+tar -xzf clusters.tar.gz
+echo -e "sample\t$( pwd )/alignment.bam" > samples.tsv
+awk -F, 'BEGIN { OFS="\t" }; NR>1 {print  "sample",$1,$2}' analysis/clustering/graphclust/clusters.csv > barcodes.tsv
+
+# clone repo
+git clone https://github.com/cellgeni/nf-scsajr
+
+# run pipeline
+nextflow run nf-scsajr \
+ --SAMPLEFILE samples.tsv \
+ --BARCODEFILE barcodes.tsv \
+ --minsamples 1 \
+ -resume
+
+# it should generate output similar to one in "output" dir (plus rds files)

examples/10x.PBMC/run.sh

@@ -1,11 +1,12 @@
 # 10k Human PBMCs, 5' v2.0, Chromium X (with intronic reads)
 # https://www.10xgenomics.com/datasets/10k-human-pbmcs-5-v2-0-chromium-x-with-intronic-reads-2-standard
-mkdir test
-cd test
+mkdir 10x.PBMC
+cd 10x.PBMC
 
-wget https://cf.10xgenomics.com/samples/cell-vdj/6.1.2/10k_PBMC_5pv2_nextgem_Chromium_X_intron_10k_PBMC_5pv2_nextgem_Chromium_X_intron/10k_PBMC_5pv2_nextgem_Chromium_X_intron_10k_PBMC_5pv2_nextgem_Chromium_X_intron_count_sample_alignments.bam -O alignment.bam
-wget https://cf.10xgenomics.com/samples/cell-vdj/6.1.2/10k_PBMC_5pv2_nextgem_Chromium_X_intron_10k_PBMC_5pv2_nextgem_Chromium_X_intron/10k_PBMC_5pv2_nextgem_Chromium_X_intron_10k_PBMC_5pv2_nextgem_Chromium_X_intron_count_sample_alignments.bam.bai -O alignment.bam.bai
-wget https://cf.10xgenomics.com/samples/cell-vdj/6.1.2/10k_PBMC_5pv2_nextgem_Chromium_X_intron_10k_PBMC_5pv2_nextgem_Chromium_X_intron/10k_PBMC_5pv2_nextgem_Chromium_X_intron_10k_PBMC_5pv2_nextgem_Chromium_X_intron_count_analysis.tar.gz -O clusters.tar.gz
+path="https://cf.10xgenomics.com/samples/cell-vdj/6.1.2/10k_PBMC_5pv2_nextgem_Chromium_X_intron_10k_PBMC_5pv2_nextgem_Chromium_X_intron/10k_PBMC_5pv2_nextgem_Chromium_X_intron_10k_PBMC_5pv2_nextgem_Chromium_X_intron_count"
+wget ${path}_sample_alignments.bam -O alignment.bam
+wget ${path}_sample_alignments.bam.bai -O alignment.bam.bai
+wget ${path}_analysis.tar.gz -O clusters.tar.gz
 
 # prepare input files
 tar -xzf clusters.tar.gz
@@ -22,3 +23,4 @@ nextflow run nf-scsajr \
  --minsamples 1 \
  -resume
 
+# it should generate output similar to one in "output" dir (plus rds files)