From f12ed55d1d29730896ee9e2d7aa6b221dcf36e3f Mon Sep 17 00:00:00 2001
From: dpryan79 <dpryan79@gmail.com>
Date: Tue, 10 Jul 2018 16:48:13 +0200
Subject: [PATCH 1/2] We need this file

---
 .../scRNAseq/celseq_barcodes.192.txt          | 192 ++++++++++++++++++
 1 file changed, 192 insertions(+)
 create mode 100644 snakePipes/workflows/scRNAseq/celseq_barcodes.192.txt

diff --git a/snakePipes/workflows/scRNAseq/celseq_barcodes.192.txt b/snakePipes/workflows/scRNAseq/celseq_barcodes.192.txt
new file mode 100644
index 000000000..7024d6e5a
--- /dev/null
+++ b/snakePipes/workflows/scRNAseq/celseq_barcodes.192.txt
@@ -0,0 +1,192 @@
+1	AGTGTC
+2	ACCATG
+3	GAGTGA
+4	CACTCA
+5	CATGTC
+6	ACAGGA
+7	GTACCA
+8	ACAGAC
+9	ACGTTG
+10	ACCAAC
+11	GTGAAG
+12	CACTTC
+13	GAGTTG
+14	GAAGAC
+15	TGCAGA
+16	CTAGGA
+17	ACCAGA
+18	GTGACA
+19	CTAGAC
+20	AGCTCA
+21	ACTCGA
+22	CTGTTG
+23	CATGCA
+24	CAGAAG
+25	GTCTCA
+26	GTGATC
+27	TGTCTG
+28	GACAGA
+29	ACTCTG
+30	TGCAAC
+31	GAAGGA
+32	GTTGAG
+33	AGACCA
+34	TGGTTG
+35	GATCTG
+36	CTAGTG
+37	CTCAGA
+38	CTTCGA
+39	AGCTAG
+40	GATCGA
+41	GTACTC
+42	TGTCGA
+43	ACGTGA
+44	AGGATC
+45	CTCATG
+46	AGACTC
+47	GACAAC
+48	AGGACA
+49	ACTCAC
+50	GTACAG
+51	AGGAAG
+52	AGTGCA
+53	TGGTGA
+54	AGACAG
+55	AGCTTC
+56	TGAGGA
+57	ACGTAC
+58	TCACAG
+59	ACAGTG
+60	CGATTG
+61	TCTTGC
+62	GGTAAC
+63	TCATCC
+64	TAGGAC
+65	TTCACC
+66	AACGAG
+67	GTGGAA
+68	ATGTCG
+69	ATCACG
+70	GAATCC
+71	CGATGA
+72	GAATGG
+73	GCAACA
+74	TTCTCG
+75	ATTGCG
+76	TAGTGG
+77	AAGCCA
+78	CTATCC
+79	TCCGAA
+80	TGAACC
+81	TGTACG
+82	GACGAA
+83	CCACAA
+84	CACCAA
+85	CTAAGC
+86	GATACG
+87	ACAAGC
+88	TGAAGG
+89	TAACGG
+90	AACCTC
+91	CGTCTA
+92	CCATAG
+93	TTCCAG
+94	GGACAA
+95	ACTTCG
+96	TTGTGC
+97	GGTATG
+98	CTGCTA
+99	ATGAGG
+100	GGTAGA
+101	ATCGTG
+102	ATGGAC
+103	AGTAGG
+104	CCATCA
+105	AGTACC
+106	CCAGTA
+107	CGTTAC
+108	GAGGTA
+109	TTGGCA
+110	CAATGC
+111	GCGTTA
+112	TAGCTC
+113	TTCGAC
+114	GAGCAA
+115	TTGCTG
+116	TTGCGA
+117	GCAGAA
+118	CCTACA
+119	GCATGA
+120	AACTGG
+121	CGGTTA
+122	CTAACG
+123	CACGTA
+124	TTGGAG
+125	GCAATG
+126	TATCCG
+127	ATGCAG
+128	GCTCTA
+129	ATTCGC
+130	TGTTGG
+131	ATGACC
+132	CCGTAA
+133	TGATCG
+134	TACAGG
+135	AGAACG
+136	GCCATA
+137	ACGGTA
+138	AAGCAC
+139	CGAACA
+140	ATGCTC
+141	GGCTTA
+142	ATCGCA
+143	GGATCA
+144	CCAATC
+145	AAGGTG
+146	ATCTCC
+147	GTATCG
+148	TGTTCC
+149	GGTGTA
+150	TACTCC
+151	ATCAGC
+152	AAGTGC
+153	AGGCTA
+154	CCTATG
+155	TATCGC
+156	CGCTAA
+157	GTAACC
+158	ACATGG
+159	CCGATA
+160	GGATAC
+161	GTTAGG
+162	TACGCA
+163	AGATGC
+164	TTGCAC
+165	CAGGAA
+166	TCTAGG
+167	GCTTCA
+168	TTGGTC
+169	TACCGA
+170	CATTGG
+171	CTCGAA
+172	GCTTAC
+173	ATACGG
+174	GTATGC
+175	TGTAGC
+176	CGTAAG
+177	TTACGC
+178	TACCAC
+179	CGCATA
+180	GCTAAG
+181	ATCCAC
+182	CCTTGA
+183	AGCGAA
+184	GGTTAG
+185	GATTGC
+186	CGTTCA
+187	ATCCGA
+188	GCATTC
+189	CCTGAA
+190	GGAATC
+191	TCAACG
+192	AACACC

From 3d2f0be2a656f4943d751ef75b9386575da28cc4 Mon Sep 17 00:00:00 2001
From: dpryan79 <dpryan79@gmail.com>
Date: Wed, 11 Jul 2018 08:41:18 +0200
Subject: [PATCH 2/2] png output isn't currently supported, it's a known bug

---
 snakePipes/workflows/scRNAseq/scRNAseq_QC_metrics2.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/snakePipes/workflows/scRNAseq/scRNAseq_QC_metrics2.R b/snakePipes/workflows/scRNAseq/scRNAseq_QC_metrics2.R
index 8ab3c4438..d7f49f270 100644
--- a/snakePipes/workflows/scRNAseq/scRNAseq_QC_metrics2.R
+++ b/snakePipes/workflows/scRNAseq/scRNAseq_QC_metrics2.R
@@ -119,7 +119,7 @@ libs_per_plate = 2
 if (is_split_library) libs_per_plate = 4
 
 
-png(file=paste(out_prefix,".reads_UMI_plot.png",sep=""),width=1500,height=1500)
+pdf(file=paste(out_prefix,".reads_UMI_plot.pdf",sep=""))
 ggplot(dat=sc_dat,aes(x=(READS_UNIQFEAT),y=(UMI),color=sample))+geom_point(size=3,alpha=0.8) + 
 	facet_wrap(~sample,ncol=libs_per_plate)+
 	xlab("reads on feature per cell")+
@@ -148,7 +148,7 @@ if (num_samples>4){
 
 print(height)
 
-png(file=paste(out_prefix,".plate_cUPM.png",sep=""),width=1000,height=height)
+pdf(file=paste(out_prefix,".plate_cUPM.pdf",sep=""))
 
 ggplot(sc_dat,aes(x=x,y=y,fill=cUPM_zscore))+ 
 		geom_tile() + 
@@ -165,7 +165,7 @@ ggplot(sc_dat,aes(x=x,y=y,fill=cUPM_zscore))+
 
 dev.off()
 
-png(file=paste(out_prefix,".plate_cRPM.png",sep=""),width=1000,height=height)
+pdf(file=paste(out_prefix,".plate_cRPM.png",sep="")) #,width=1000,height=height)
 
 ggplot(sc_dat,aes(x=x,y=y,fill=cRPM_zscore))+ 
 		geom_tile() + 
@@ -182,7 +182,7 @@ ggplot(sc_dat,aes(x=x,y=y,fill=cRPM_zscore))+
 dev.off()
 
 
-png(file=paste(out_prefix,".plate_abs_transcripts.png",sep=""),width=1000,height=height)
+pdf(file=paste(out_prefix,".plate_abs_transcripts.png",sep="")) #,width=1000,height=height)
 
 ggplot(sc_dat,aes(x=x,y=y,fill=UMI))+ 
 		geom_tile() +