Snakefile

@@ -561,7 +561,7 @@ rule extract_transcripts_as_bed12:
             )
 
     singularity:
-        "docker://zavolab/zgtf:0.1"
+        "docker://quay.io/biocontainers/zgtf:0.1.1--pyh5e36f6f_0"
 
     threads: 1
 
@@ -698,10 +698,10 @@ rule calculate_TIN_scores:
     threads: 8
 
     singularity:
-        "docker://zavolab/tin_score_calculation:0.2.0-slim"
+        "docker://quay.io/biocontainers/tin-score-calculation:0.4--pyh5e36f6f_0"
 
     shell:
-        "(tin_score_calculation.py \
+        "(calculate-tin.py \
         -i {input.bam} \
         -r {input.transcripts_bed12} \
         --names {params.sample} \
@@ -944,7 +944,7 @@ rule kallisto_merge_genes:
     threads: 1
 
     singularity:
-        "docker://zavolab/merge_kallisto:0.6"
+        "docker://quay.io/biocontainers/r-merge-kallisto:0.6--hdfd78af_0"
 
     shell:
         "(merge_kallisto.R \
@@ -1025,7 +1025,7 @@ rule kallisto_merge_transcripts:
     threads: 1
 
     singularity:
-        "docker://zavolab/merge_kallisto:0.6"
+        "docker://quay.io/biocontainers/r-merge-kallisto:0.6--hdfd78af_0"
 
     shell:
         "(merge_kallisto.R \
@@ -1072,7 +1072,7 @@ rule pca_salmon:
     threads: 1
 
     singularity:
-        "docker://zavolab/zpca:0.8.3-1"
+        "docker://quay.io/biocontainers/zpca:0.8.3.post1--pyh5e36f6f_0"
 
     shell:
         "(zpca-tpm  \
@@ -1118,7 +1118,7 @@ rule pca_kallisto:
     threads: 1
 
     singularity:
-        "docker://zavolab/zpca:0.8.3-1"
+        "docker://quay.io/biocontainers/zpca:0.8.3.post1--pyh5e36f6f_0"
 
     shell:
         "(zpca-tpm  \