fix: handling of <output_dir> input argument (#163)

bihealth · Apr 28, 2023 · bdf0e21 · bdf0e21
1 parent ae8bb92
commit bdf0e21
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Showing 48 changed files with 54 additions and 50 deletions.
diff --git a/cubi_tk/isa_tpl/__init__.py b/cubi_tk/isa_tpl/__init__.py
@@ -176,8 +176,8 @@ def run_cookiecutter(tpl, args, _parser=None, _subparser=None, no_input=False):
     logger.info(args)
 
     output_dir = os.path.realpath(args.output_dir)
-    output_base = os.path.dirname(args.output_dir)
-    extra_context["i_dir_name"] = os.path.basename(output_dir)
+    output_base = os.path.dirname(output_dir)
+    extra_context["__output_dir"] = os.path.basename(output_dir)
 
     # FIXME: better solution? (added because args.var_is_triplet is None)
     if "is_triplet" in tpl.configuration:

diff --git a/cubi_tk/isa_tpl/isatab-bulk_rnaseq/cookiecutter.json b/cubi_tk/isa_tpl/isatab-bulk_rnaseq/cookiecutter.json
@@ -9,9 +9,9 @@
   "center_contact": "",
 
   "study_title": "{{cookiecutter.investigation_title}}",
-  "i_dir_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
-  "s_file_name": "{{cookiecutter.i_dir_name}}",
-  "assay_prefix": "{{cookiecutter.i_dir_name|lower}}",
+  "s_file_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
+  "assay_prefix": "{{cookiecutter.s_file_name|lower}}",
   "a_technology_type": "nucleotide sequencing",
-  "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}"
+  "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}",
+  "__output_dir": "Required variable. Do not remove."
 }
diff --git a/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt b/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt
diff --git a/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt b/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt
@@ -32,7 +32,7 @@ Investigation Person Roles
 Investigation Person Roles Term Accession Number
 Investigation Person Roles Term Source REF
 STUDY
-Study Identifier	{{cookiecutter.i_dir_name}}
+Study Identifier	{{cookiecutter.s_file_name}}
 Study Title	{{cookiecutter.investigation_title}}
 Study Description	""
 Comment[Study Grant Number]	""

diff --git a/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt b/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt
diff --git a/cubi_tk/isa_tpl/isatab-generic/cookiecutter.json b/cubi_tk/isa_tpl/isatab-generic/cookiecutter.json
@@ -46,13 +46,13 @@
   "center_contact": "",
 
   "study_title": "{{cookiecutter.investigation_title}}",
-  "i_dir_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
-  "s_file_name": "{{cookiecutter.i_dir_name}}",
-  "assay_prefix": "{{cookiecutter.i_dir_name|lower}}",
+  "s_file_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
+  "assay_prefix": "{{cookiecutter.s_file_name|lower}}",
   "a_measurement_abbreviation": "{% if cookiecutter.a_measurement_type == 'transcription profiling' %}mRNA_seq{% else %}UNKNOWN{% endif %}",
   "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}",
   "sample_type": "x-charite-medgen-blood-book-id",
   "lib_strategy": "{% if cookiecutter.a_measurement_abbreviation == 'mRNA_seq' %}RNA-seq{% else %}UNKNOWN{% endif %}",
   "lib_selection": "{% if cookiecutter.a_measurement_abbreviation == 'mRNA_seq' %}PolyA{% else %}UNKNOWN{% endif %}",
-  "lib_layout": [ "PAIRED", "SINGLE" ]
+  "lib_layout": [ "PAIRED", "SINGLE" ],
+  "__output_dir": "Required variable. Do not remove."
 }
diff --git a/...~lock.s_{{cookiecutter.s_file_name}}.txt# → ...~lock.s_{{cookiecutter.s_file_name}}.txt# b/...~lock.s_{{cookiecutter.s_file_name}}.txt# → ...~lock.s_{{cookiecutter.s_file_name}}.txt#
diff --git a/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt b/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt
diff --git a/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt b/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt
@@ -30,7 +30,7 @@ Investigation Person Roles
 Investigation Person Roles Term Accession Number
 Investigation Person Roles Term Source REF
 STUDY
-Study Identifier	{{cookiecutter.i_dir_name}}
+Study Identifier	{{cookiecutter.s_file_name}}
 Study Title	{{cookiecutter.investigation_title}}
 Study Description	""
 Comment[Study Grant Number]	""

diff --git a/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt b/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt
diff --git a/cubi_tk/isa_tpl/isatab-germline/cookiecutter.json b/cubi_tk/isa_tpl/isatab-germline/cookiecutter.json
@@ -61,14 +61,14 @@
   "center_contact": "",
 
   "study_title": "{{cookiecutter.investigation_title}}",
-  "i_dir_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
-  "s_file_name": "{{cookiecutter.i_dir_name}}",
-  "assay_prefix": "{{cookiecutter.i_dir_name|lower}}",
+  "s_file_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
+  "assay_prefix": "{{cookiecutter.s_file_name|lower}}",
   "a_technology_type": "nucleotide sequencing",
   "a_measurement_abbreviation": "{% if cookiecutter.a_measurement_type == 'exome sequencing' %}WES{% else %}WGS{% endif %}",
   "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}",
   "sample_type": "x-charite-medgen-blood-book-id",
   "lib_strategy": "{% if cookiecutter.a_measurement_abbreviation == 'WES' %}WXS{% else %}WGS{% endif %}",
   "lib_selection": "{% if cookiecutter.a_measurement_abbreviation == 'WES' %}Hybrid Selection{% else %}RANDOM{% endif %}",
-  "lib_layout": "PAIRED"
+  "lib_layout": "PAIRED",
+  "__output_dir": "Required variable. Do not remove."
 }
diff --git a/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt b/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt
diff --git a/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt b/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt
@@ -32,7 +32,7 @@ Investigation Person Roles
 Investigation Person Roles Term Accession Number
 Investigation Person Roles Term Source REF
 STUDY
-Study Identifier	{{cookiecutter.i_dir_name}}
+Study Identifier	{{cookiecutter.s_file_name}}
 Study Title	{{cookiecutter.investigation_title}}
 Study Description	""
 Comment[Study Grant Number]	""

diff --git a/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt b/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt
diff --git a/cubi_tk/isa_tpl/isatab-microarray/cookiecutter.json b/cubi_tk/isa_tpl/isatab-microarray/cookiecutter.json
@@ -22,9 +22,8 @@
   "array_design_ref": "",
 
   "study_title": "{{cookiecutter.investigation_title}}",
-  "i_dir_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
-  "s_file_name": "{{cookiecutter.i_dir_name}}",
-  "assay_prefix": "{{cookiecutter.i_dir_name|lower}}",
+  "s_file_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
+  "assay_prefix": "{{cookiecutter.s_file_name|lower}}",
   "a_technology_type": "microarray",
   "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}",
 
@@ -37,5 +36,6 @@
       "accession_number": "http://purl.obolibrary.org/obo/OBI_0400148",
       "source_ref": "OBI"
     }
-  }
+  },
+  "__output_dir": "Required variable. Do not remove."
 }
diff --git a/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt b/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt
diff --git a/...iecutter.i_dir_name}}/i_investigation.txt → ...cutter.__output_dir}}/i_investigation.txt b/...iecutter.i_dir_name}}/i_investigation.txt → ...cutter.__output_dir}}/i_investigation.txt
@@ -32,7 +32,7 @@ Investigation Person Roles
 Investigation Person Roles Term Accession Number	
 Investigation Person Roles Term Source REF	
 STUDY
-Study Identifier	{{cookiecutter.i_dir_name}}
+Study Identifier	{{cookiecutter.s_file_name}}
 Study Title	{{cookiecutter.investigation_title}}
 Study Description	""
 Comment[Study Grant Number]	""

diff --git a/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt b/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt
diff --git a/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/cookiecutter.json b/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/cookiecutter.json
@@ -1,6 +1,5 @@
 {
   "investigation_title": "Investigation Title",
-  "i_dir_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
 
   "study_title": "{{cookiecutter.investigation_title}}",
   "study_id": "{{cookiecutter.study_title|lower|replace(' ', '_')}}",
@@ -77,5 +76,6 @@
   "chromatography_instrument": [
     "Agilent UHPLC 1290",
     "Agilent 1290 Infinity II LC System"
-  ]
+  ],
+  "__output_dir": "Required variable. Do not remove."
 }
diff --git a/...fix}}_{{cookiecutter.assay_name}}_FIA.txt → ...fix}}_{{cookiecutter.assay_name}}_FIA.txt b/...fix}}_{{cookiecutter.assay_name}}_FIA.txt → ...fix}}_{{cookiecutter.assay_name}}_FIA.txt
diff --git a/...efix}}_{{cookiecutter.assay_name}}_LC.txt → ...efix}}_{{cookiecutter.assay_name}}_LC.txt b/...efix}}_{{cookiecutter.assay_name}}_LC.txt → ...efix}}_{{cookiecutter.assay_name}}_LC.txt
diff --git a/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt b/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt
diff --git a/...}}/s_{{cookiecutter.study_file_name}}.txt → ...}}/s_{{cookiecutter.study_file_name}}.txt b/...}}/s_{{cookiecutter.study_file_name}}.txt → ...}}/s_{{cookiecutter.study_file_name}}.txt
diff --git a/cubi_tk/isa_tpl/isatab-single_cell_rnaseq/cookiecutter.json b/cubi_tk/isa_tpl/isatab-single_cell_rnaseq/cookiecutter.json
@@ -27,9 +27,9 @@
   "sample_multiplexing": ["No", "CellPlex", "TotalSeq", "Other"],
   "genotype_multiplexing": ["no", "yes"],
   "study_title": "{{cookiecutter.investigation_title}}",
-  "i_dir_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
-  "s_file_name": "{{cookiecutter.i_dir_name}}",
-  "assay_prefix": "{{cookiecutter.i_dir_name|lower}}",
+  "s_file_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
+  "assay_prefix": "{{cookiecutter.s_file_name|lower}}",
   "a_technology_type": "nucleotide sequencing",
-  "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}"
-}
+  "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}",
+  "__output_dir": "Required variable. Do not remove."
+}
diff --git a/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt b/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt
diff --git a/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt b/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt
@@ -32,7 +32,7 @@ Investigation Person Roles
 Investigation Person Roles Term Accession Number
 Investigation Person Roles Term Source REF
 STUDY
-Study Identifier	{{cookiecutter.i_dir_name}}
+Study Identifier	{{cookiecutter.s_file_name}}
 Study Title	{{cookiecutter.investigation_title}}
 Study Description	""
 Comment[Study Grant Number]	""

diff --git a/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt b/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt
diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core/cookiecutter.json b/cubi_tk/isa_tpl/isatab-stem_cell_core/cookiecutter.json
@@ -12,9 +12,9 @@
   "library_construction_meta": "{{'Sequencing kit,RNA amount,QC cell load recovery,QC tape fragment size' if cookiecutter.library_type == 'Single-Cell' else 'Sequencing kit,RNA amount,QC tape fragment size'}}",
   "sequencing_meta": "Platform,Instrument model,No. targeted reads,QC-notes",
   "study_title": "{{cookiecutter.investigation_title}}",
-  "i_dir_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
-  "s_file_name": "{{cookiecutter.i_dir_name}}",
-  "assay_prefix": "{{cookiecutter.i_dir_name|lower}}",
+  "s_file_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
+  "assay_prefix": "{{cookiecutter.s_file_name|lower}}",
   "a_technology_type": "nucleotide sequencing",
-  "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}"
+  "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}",
+  "__output_dir": "Required variable. Do not remove."
 }
diff --git a/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt b/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt
diff --git a/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt b/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt
@@ -32,7 +32,7 @@ Investigation Person Roles
 Investigation Person Roles Term Accession Number
 Investigation Person Roles Term Source REF
 STUDY
-Study Identifier	{{cookiecutter.i_dir_name}}
+Study Identifier	{{cookiecutter.s_file_name}}
 Study Title	{{cookiecutter.investigation_title}}
 Study Description	""
 Comment[Study Grant Number]	""

diff --git a/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt b/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt
diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/cookiecutter.json b/cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/cookiecutter.json
@@ -13,8 +13,8 @@
   "library_kit": "mRNA",
   "library_construction_meta": "Library selection,Target insert size",
   "sequencing_meta": "Platform,Instrument model,No. targeted reads,Paired-End",
-  "i_dir_name": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}",
   "s_file_name": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}",
   "assay_prefix": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}",
-  "assay_name": "GEX_{{cookiecutter.a_measurement_type|replace(' ', '_')}}"
+  "assay_name": "GEX_{{cookiecutter.a_measurement_type|replace(' ', '_')}}",
+  "__output_dir": "Required variable. Do not remove."
 }
diff --git a/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt b/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt
diff --git a/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt b/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt
@@ -32,7 +32,7 @@ Investigation Person Roles
 Investigation Person Roles Term Accession Number
 Investigation Person Roles Term Source REF
 STUDY
-Study Identifier	{{cookiecutter.i_dir_name}}
+Study Identifier	{{cookiecutter.s_file_name}}
 Study Title	{{cookiecutter.investigation_title}}
 Study Description	""
 Comment[Study Grant Number]	""

diff --git a/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt b/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt
diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core_sc/cookiecutter.json b/cubi_tk/isa_tpl/isatab-stem_cell_core_sc/cookiecutter.json
@@ -32,8 +32,8 @@
   "library_type": ["GEX", "GEX+antibody", "GEX+VDJ", "GEX+other", "GEX+antibody+VDJ", "GEX+other+another"],
   "sample_multiplexing": ["No", "CellPlex", "TotalSeq", "Other"],
   "genotype_multiplexing": ["no", "yes"],
-  "i_dir_name": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}",
   "s_file_name": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}",
   "assay_prefix": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}",
-  "assay_name": "{{cookiecutter.library_type}}_{{cookiecutter.a_measurement_type|replace(' ', '_')}}"
+  "assay_name": "{{cookiecutter.library_type}}_{{cookiecutter.a_measurement_type|replace(' ', '_')}}",
+  "__output_dir": "Required variable. Do not remove."
 }
diff --git a/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt b/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt
diff --git a/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt b/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt
@@ -32,7 +32,7 @@ Investigation Person Roles
 Investigation Person Roles Term Accession Number
 Investigation Person Roles Term Source REF
 STUDY
-Study Identifier	{{cookiecutter.i_dir_name}}
+Study Identifier	{{cookiecutter.s_file_name}}
 Study Title	{{cookiecutter.investigation_title}}
 Study Description	""
 Comment[Study Grant Number]	""

diff --git a/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt b/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt
diff --git a/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt b/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt
diff --git a/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt b/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt
diff --git a/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt b/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt
diff --git a/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/cookiecutter.json b/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/cookiecutter.json
@@ -55,10 +55,9 @@
   "center_contact": "",
 
   "study_title": "{{cookiecutter.investigation_title}}",
-  "i_dir_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
   "is_triplet": null,
-  "s_file_name": "{{cookiecutter.i_dir_name}}",
-  "assay_prefix": "{{cookiecutter.i_dir_name|lower}}",
+  "s_file_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
+  "assay_prefix": "{{cookiecutter.s_file_name|lower}}",
   "a_technology_type": "nucleotide sequencing",
   "a_measurement_abbreviation": "{% if cookiecutter.a_measurement_type == 'exome sequencing' %}WES{% else %}WGS{% endif %}",
   "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}",
@@ -68,5 +67,6 @@
   "lib_layout": [
     "PAIRED",
     "SINGLE"
-  ]
+  ],
+  "__output_dir": "Required variable. Do not remove."
 }
diff --git a/...ptome_profiling_nucleotide_sequencing.txt → ...ptome_profiling_nucleotide_sequencing.txt b/...ptome_profiling_nucleotide_sequencing.txt → ...ptome_profiling_nucleotide_sequencing.txt
diff --git a/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt b/..._prefix}}_{{cookiecutter.assay_name}}.txt → ..._prefix}}_{{cookiecutter.assay_name}}.txt
diff --git a/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt b/...iecutter.i_dir_name}}/i_Investigation.txt → ...cutter.__output_dir}}/i_Investigation.txt
@@ -32,7 +32,7 @@ Investigation Person Roles
 Investigation Person Roles Term Accession Number
 Investigation Person Roles Term Source REF
 STUDY
-Study Identifier	{{cookiecutter.i_dir_name}}
+Study Identifier	{{cookiecutter.s_file_name}}
 Study Title	{{cookiecutter.investigation_title}}
 Study Description	""
 Comment[Study Grant Number]	""

diff --git a/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt b/...name}}/s_{{cookiecutter.s_file_name}}.txt → ..._dir}}/s_{{cookiecutter.s_file_name}}.txt
diff --git a/tests/test_isa_tpl.py b/tests/test_isa_tpl.py
@@ -22,8 +22,10 @@ def test_run_cookiecutter_isatab_generic(tmp_path):
 
     assert output_path.exists()
     assert (output_path / "i_Investigation.txt").exists()
-    assert (output_path / "a_output_dir_transcription_profiling_nucleotide_sequencing.txt").exists()
-    assert (output_path / "s_output_dir.txt").exists()
+    assert (
+        output_path / "a_investigation_title_transcription_profiling_nucleotide_sequencing.txt"
+    ).exists()
+    assert (output_path / "s_Investigation_Title.txt").exists()
 
 
 def test_run_cookiecutter_isatab_germline(tmp_path):
@@ -36,8 +38,10 @@ def test_run_cookiecutter_isatab_germline(tmp_path):
 
     assert output_path.exists()
     assert (output_path / "i_Investigation.txt").exists()
-    assert (output_path / "a_output_dir_exome_sequencing_nucleotide_sequencing.txt").exists()
-    assert (output_path / "s_output_dir.txt").exists()
+    assert (
+        output_path / "a_investigation_title_exome_sequencing_nucleotide_sequencing.txt"
+    ).exists()
+    assert (output_path / "s_Investigation_Title.txt").exists()
 
 
 def test_run_cookiecutter_isatab_ms_meta_biocrates(tmp_path):