From d34bfeb267d6c675adb2c41b4da041fef24afd12 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 26 Apr 2024 14:59:20 -0400
Subject: [PATCH] refactor: switch nclscan container to star_ucsc_cufflinks
 everywhere

---
 config/config.yaml                    | 3 +--
 docker/star_ucsc_cufflinks/Dockerfile | 1 -
 workflow/rules/align.smk              | 2 +-
 workflow/rules/findcircrna.smk        | 6 +++---
 4 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/config/config.yaml b/config/config.yaml
index fb67226..cc0652c 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -124,9 +124,8 @@ containers:
   fastqc: 'docker://nciccbr/ccrgb_qctools:v4.0'
   mapsplice: "docker://cgrlab/mapsplice2:latest"
   multiqc: 'docker://nciccbr/ccbr_multiqc_1.15:v1'
-  nclscan: "docker://nciccbr/charlie_nclscan:v0.1.0"
   picard: 'docker://nciccbr/ccbr_picard_2.27.5:v1'
   R: 'docker://nciccbr/ccbr_r_4.3.0:v1'
   star: "docker://nciccbr/ccbr_star_2.7.6a:latest"
-  star_ucsc_cufflinks: "docker://nciccbr/charlie_star_ucsc_cufflinks:v0.1.0"
+  star_ucsc_cufflinks: "docker://nciccbr/charlie_star_ucsc_cufflinks:v0.2.0"
   ucsc: 'docker://nciccbr/ccbr_ucsc:v1'
diff --git a/docker/star_ucsc_cufflinks/Dockerfile b/docker/star_ucsc_cufflinks/Dockerfile
index eae3f40..4c7ff18 100644
--- a/docker/star_ucsc_cufflinks/Dockerfile
+++ b/docker/star_ucsc_cufflinks/Dockerfile
@@ -26,7 +26,6 @@ ENV PATH="/opt2/NCLscan-${NCLSCAN_VERSION}/:/opt2/NCLscan-${NCLSCAN_VERSION}/bin
 
 # Save Dockerfile in the docker
 COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
-RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
 
 # cleanup
 WORKDIR /data2
diff --git a/workflow/rules/align.smk b/workflow/rules/align.smk
index f3e5daa..f6c2e92 100644
--- a/workflow/rules/align.smk
+++ b/workflow/rules/align.smk
@@ -570,7 +570,7 @@ rule find_circ_align:
         peorse=get_peorse,
         find_circ_dir=FIND_CIRC_DIR,
         randomstr=str(uuid.uuid4()),
-    container: config['containers']["nclscan"]
+    container: config['containers']['star_ucsc_cufflinks']
     threads: getthreads("find_circ_align")
     shell:
         """
diff --git a/workflow/rules/findcircrna.smk b/workflow/rules/findcircrna.smk
index 8a832f7..662b109 100644
--- a/workflow/rules/findcircrna.smk
+++ b/workflow/rules/findcircrna.smk
@@ -941,7 +941,7 @@ rule mapsplice_postprocess:
         bai=join(
             WORKDIR, "results", "{sample}", "MapSplice", "{sample}.mapsplice.cram.crai"
         ),
-    container: config['containers']["nclscan"]
+    container: config['containers']['star_ucsc_cufflinks']
     params:
         script=join(SCRIPTS_DIR, "create_mapsplice_per_sample_counts_table.py"),
         memG=getmemG("mapsplice_postprocess"),
@@ -1031,7 +1031,7 @@ rule nclscan:
             "NCLscan",
             "{sample}.nclscan.counts_table.tsv.filtered",
         ),
-    container: config['containers']["nclscan"]
+    container: config['containers']['star_ucsc_cufflinks']
     threads: getthreads("nclscan")
     params:
         workdir=WORKDIR,
@@ -1205,7 +1205,7 @@ rule find_circ:
         min_reads=config['circexplorer_bsj_circRNA_min_reads'],
         collapse_script=join(SCRIPTS_DIR,"_collapse_find_circ.py"),
         randomstr=str(uuid.uuid4()),
-    container: config['containers']["nclscan"]
+    container: config['containers']['star_ucsc_cufflinks']
     threads: getthreads("find_circ")
     shell:
         """