Merge pull request #1282 from grennfp/main

change ERCC92 download link and collapse_annotation.py fix

Author: gaow

code/reference_data/reference_data_preparation.ipynb

@@ -944,7 +944,7 @@
     "[download_ercc_reference]\n",
     "output: f\"{cwd:a}/ERCC92.gtf\", f\"{cwd:a}/ERCC92.fa\"\n",
     "download: dest_dir = cwd, decompress=True\n",
-    "    https://tools.thermofisher.com/content/sfs/manuals/ERCC92.zip"
+    "    https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip"
    ]
   },
   {
@@ -1168,7 +1168,7 @@
     "output: f'{_input:n}{\".collapse_only\" if stranded else \"\"}.gene.gtf'\n",
     "task: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, tags = f'{step_name}_{_output:bn}'\n",
     "bash: expand = \"${ }\", stderr = f'{_output}.stderr', stdout = f'{_output}.stdout', container = container, entrypoint = entrypoint\n",
-    "    collapse_annotation.py ${\"--collapse_only\" if stranded else \"\"} ${_input} ${_output}"
+    "    collapse_annotation ${\"--collapse_only\" if stranded else \"\"} ${_input} ${_output}"
    ]
   },
   {