From 55a2092f42693ddece6d20c0337353a95504b382 Mon Sep 17 00:00:00 2001 From: saeidamiri1 Date: Tue, 20 Feb 2024 10:55:57 -0500 Subject: [PATCH] Built on 2024-02-20, v0.1.53.3 --- .DS_Store | Bin 12292 -> 10244 bytes scrnabox.pip/.DS_Store | Bin 6148 -> 6148 bytes scrnabox.pip/hto/.DS_Store | Bin 6148 -> 6148 bytes scrnabox.pip/hto/pars/step1_par.txt | 2 +- scrnabox.pip/hto/scripts/.DS_Store | Bin 6148 -> 6148 bytes .../scripts/step1/create_cellranger_hto.sh | 6 +++--- .../step1/create_cellranger_hto_local.sh | 4 ++-- scrnabox.pip/scrna/pars/step1_par.txt | 2 +- .../scripts/step1/create_cellranger_scrna.sh | 6 +++--- .../step1/create_cellranger_scrna_local.sh | 2 +- 10 files changed, 11 insertions(+), 11 deletions(-) diff --git a/.DS_Store b/.DS_Store index 8eecb2ccbb7321a33fbd1ad1dc34e3a37fa86e0d..cb8ec386177fa1014a2e6542640eb9bb7831e514 100644 GIT binary patch delta 216 zcmZokXbF&DU|?W$DortDU{C-uIe-{M3-C-V6q~3gIoUvmMHI+qFau&npg2QLx?yl~ zes00$M9Ecb6C3_=0!2Z9gBvI!&azpZ=Ls{T*=8PvVpfin;^ds9{QR8B|AfRhKNgZ_ zL=|BY(dHCnhG`N zTab_yQ+yCLlJ%b0XwU~^B&k(njJL%XFoMR*nVl{vgz#vb%_)5kK6iwT@)AzeY+^L3q^y=FG%NeipnY~Yc@7CZ|&&r-LtqV zH!sO$xu9?;Vc15{)JHTsq+4ObIx;wIgk$5QMp(CE#$iK`N>V-!3|QKvzR2@(R~45i z%5Xer9E}^XKcjhcMpX{1A8K2r!t)WMN!l{89V62yP~?dyJ0!0RId{i z+JG%K;jSUq)=3h#2PO<_sa6iuGl_=>O)aRK?sD>$CK2izO6XDBh*(R(yW5y(vu-#P znVb}j+e?q$*3KATc))r1Zq1JEozksLTS;ZxcE(2SaV@IvowoF7rlg0lF`k!>J2l;5 zBNmCKx4uhNlo4mGj&N8HJ3G(I<;q^=KE}TkHQcZgMob)oI2d8#Hmhvk;GRSJ@2hMN zxSk{sEKLex+Np;QkuJzNPEXLwG)r&Md-O3a&=+)pzM*gF5`9m<&~NlRU8QUAzzZK% zpaA7iu?8E^h|So7W^6?_c3>xZaW952j1e4!hKDc#6BZIk;t`y}44%Yucpfj{CG@?4 zw=s`*@Cg?189v8F{D{lAf?x3m{={GS+mr8E?YYC__pEo@_Bil6*N|&6ch81YpkPsm zDXkx2SoWM&;+tQW^Mki@t?+LrmZ>GN9KDrT)Ezr}{(G@p$Z?3yUtLgGw8qg)Q(JrT zI#@1>8TyuEod)>^{?j0*kN#!?g@{VaP27~?PyMGWyYyc4JJsG#>Wp2E{Oi)ZjGX7LJM#W}o& z*KuBe{Gp5Ebx3!)e&&vkZUxjrfs=cImezvFr^B0S2rMam~9u&{#a64;b zaN1tNmEOxLzLI6L`}@U9-PL|)>btVteM}nT%83)r&4D_9eZ%IHb^a5r4PxHf z*mClu#EL5KYTG|HVNP0+$K6Je(b%d?<4g8TDnH+vKU3O|auLaLqcz#Wb}#>u&1sjt Zsl2LQ=Nsq9k)_6~UQAspeC&VH{J$cs%y<9* diff --git a/scrnabox.pip/.DS_Store b/scrnabox.pip/.DS_Store index 34b57b9ba66c3774bbf74751de16dbbb4afa6a75..551f40402d9633758f4706b9d743ee462e8be8d9 100644 GIT binary patch delta 110 zcmZoMXfc=|#>AjHu~68Uk%57MnIVIrgdsnrI5{UNKR*X30s%}=8l(n@1sEXmn;n^t qv1|@te$2F)or9kPXb@23JM(0I5k*dr(gcvU$tFC?n`1;)FarRI#}!Zj delta 404 zcmYjN%SyvQ6ur%(olwLsVnK9Kaa(X&wOHKM9}pwDPzf_lFu`%AB&k`H(oJ`|u=FR~ zmb&o|`~rW)t#^WfUKs9~IrrS*oH?D-_oiVu3)Zv=0FVW9_YDNPY&;c!1`GvPO6aHR zihWdOnlK@P3{;SAkRX7;7$giK;(0paLUA1Z;v*5K8KplJ!?f&bjnqh;Jb01Hy^Lk! zbik53eY?hAc!?RmiNoA)xED%hES6zX2;v}|;mrMQECZDf)K~^-A@-0#f;hzS8@rQ9 zm!8sgtJ6K1wp){a7jggiY&vzw&f(GdmH#B3rFzw#&?LGnYU{t3?F~V7(^X-&SBA04 zym*NeNXxVC%eF%Z|IZzH~p$KOmZ5 A^#A|> diff --git a/scrnabox.pip/hto/.DS_Store b/scrnabox.pip/hto/.DS_Store index b199cae64254b3ab945ed5840e30219fb1beea3b..eba13223f6781b153af5c8a6f35630fbb0dc1cc4 100644 GIT binary patch delta 64 zcmZoMXfc@J&&$ZbzyQPo3=9PfB@<)xWk3S#48;t|3`Go?AVG%Wl;Y%^r2PCG#*GKv O*e70)+RV=JmmdJ6aS!eQ delta 64 zcmZoMXfc@J&&$NXz`)4BAi%(o$&fxVMt`z_2#W+eLo!1?LmopKNRXj8r8qe!DL+4l SVPcQe#*J?5o7p-3@&f?8cMv@Q diff --git a/scrnabox.pip/hto/pars/step1_par.txt b/scrnabox.pip/hto/pars/step1_par.txt index f9ae806..0a0be8f 100644 --- a/scrnabox.pip/hto/pars/step1_par.txt +++ b/scrnabox.pip/hto/pars/step1_par.txt @@ -49,7 +49,7 @@ par_automated_library_prep= "no" # CellRanger counts pipeline parameters. ################################################################################## ## Path to reference genome -par_ref_dir='/path/to/CellRanger/reference/genome' +par_ref_dir_grch='/path/to/CellRanger/reference/genome' ## Minimum number of bases to retain for R1 sequence of gene expression assay. If you want to use this parameter uncomment the line below and define your par_r1_length. #par_r1_length=20 diff --git a/scrnabox.pip/hto/scripts/.DS_Store b/scrnabox.pip/hto/scripts/.DS_Store index f5970d4b214ff0976c1d19399f117ee812aecf70..0cafafb68c5349fdee5528a877c278a89367f7fc 100644 GIT binary patch delta 56 zcmZoMXfc@Jq{zqs1WX_T2tXVl7GPj7Oes#zNy^X9Vcb|ajeTMR-(&+3md)H8KluRx CEDL-9 delta 55 zcmZoMXfc@Jq`&|IOkk3Mfe}apu>b>uVM=jwPEvk;&c?!N>=PUKCmV>cZ06?p$qxYf C!3%l- diff --git a/scrnabox.pip/hto/scripts/step1/create_cellranger_hto.sh b/scrnabox.pip/hto/scripts/step1/create_cellranger_hto.sh index 68f5600..1a19650 100644 --- a/scrnabox.pip/hto/scripts/step1/create_cellranger_hto.sh +++ b/scrnabox.pip/hto/scripts/step1/create_cellranger_hto.sh @@ -74,10 +74,10 @@ cellranger count \\ --jobmode=\${SLURM_TEMPLATE} \\ EOF -# par_ref_dir -if [[ -n "${par_ref_dir}" ]]; then +# par_ref_dir_grch +if [[ -n "${par_ref_dir_grch}" ]]; then cat <> $OUTFILE - --transcriptome=\${par_ref_dir} \\ + --transcriptome=\${par_ref_dir_grch} \\ EOF fi diff --git a/scrnabox.pip/hto/scripts/step1/create_cellranger_hto_local.sh b/scrnabox.pip/hto/scripts/step1/create_cellranger_hto_local.sh index 769a47c..f436717 100644 --- a/scrnabox.pip/hto/scripts/step1/create_cellranger_hto_local.sh +++ b/scrnabox.pip/hto/scripts/step1/create_cellranger_hto_local.sh @@ -72,9 +72,9 @@ cellranger count \\ EOF # par_ref_dir -if [[ -n "${par_ref_dir}" ]]; then +if [[ -n "${par_ref_dir_grch}" ]]; then cat <> $OUTFILE - --transcriptome=\${par_ref_dir} \\ + --transcriptome=\${par_ref_dir_grch} \\ EOF fi diff --git a/scrnabox.pip/scrna/pars/step1_par.txt b/scrnabox.pip/scrna/pars/step1_par.txt index d9505bc..5265a9a 100644 --- a/scrnabox.pip/scrna/pars/step1_par.txt +++ b/scrnabox.pip/scrna/pars/step1_par.txt @@ -27,7 +27,7 @@ par_automated_library_prep= "no" # CellRanger counts pipeline parameters. ################################################################################## ## Path to reference genome -par_ref_dir='/path/to/CellRanger/reference/genome' +par_ref_dir_grch='/path/to/CellRanger/reference/genome' ## Minimum number of bases to retain for R1 sequence of gene expression assay. If you want to use this parameter uncomment the line below and define your par_r1_length. #par_r1_length=20 diff --git a/scrnabox.pip/scrna/scripts/step1/create_cellranger_scrna.sh b/scrnabox.pip/scrna/scripts/step1/create_cellranger_scrna.sh index 01d0ef6..9093f90 100644 --- a/scrnabox.pip/scrna/scripts/step1/create_cellranger_scrna.sh +++ b/scrnabox.pip/scrna/scripts/step1/create_cellranger_scrna.sh @@ -74,10 +74,10 @@ cellranger count \\ --jobmode=\${SLURM_TEMPLATE} \\ EOF -# par_ref_dir -if [[ -n "${par_ref_dir}" ]]; then +# par_ref_dir_grch +if [[ -n "${par_ref_dir_grch}" ]]; then cat <> $OUTFILE - --transcriptome=\${par_ref_dir} \\ + --transcriptome=\${par_ref_dir_grch} \\ EOF fi diff --git a/scrnabox.pip/scrna/scripts/step1/create_cellranger_scrna_local.sh b/scrnabox.pip/scrna/scripts/step1/create_cellranger_scrna_local.sh index ac36823..b0c0939 100644 --- a/scrnabox.pip/scrna/scripts/step1/create_cellranger_scrna_local.sh +++ b/scrnabox.pip/scrna/scripts/step1/create_cellranger_scrna_local.sh @@ -72,7 +72,7 @@ cellranger count \\ --libraries=\${LIBRARY} \\ EOF -# par_ref_dir +# par_ref_dir_grch if [[ -n "${par_ref_dir_grch}" ]]; then cat <> $OUTFILE --transcriptome=\${par_ref_dir_grch} \\