Merge branch 'replace_cufflinks_image_with_gffread_image' into 'master'

Replace cufflinks image with gffread image

Closes #85

See merge request zavolan_group/pipelines/rnaseqpipeline!37

Snakefile

@@ -207,7 +207,7 @@ rule extract_transcriptome:
             config['log_dir'],
             "{organism}_extract_transcriptome.log")
     singularity:
-        "docker://zavolab/cufflinks:2.2.1"
+        "docker://zavolab/gffread:0.11.7"
     shell:
         "(gffread \
         -w {output.transcriptome} \

tests/test_integration_workflow/expected_output.md5

@@ -86,4 +86,4 @@ ea91b4f85622561158bff2f7c9c312b3  results/single_end/synthetic_10_reads_mate_1_s
 ede14ac41c10067838f375106fce4852  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.str2.out.bg
 ea91b4f85622561158bff2f7c9c312b3  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str1.out.bg
 ede14ac41c10067838f375106fce4852  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str2.out.bg
-79fc3e46b3ac1a72b80cb7bebf6058cd  results/transcriptome/homo_sapiens/transcriptome.fa
+3ce47cb1d62482c5d62337751d7e8552  results/transcriptome/homo_sapiens/transcriptome.fa