remove exit code

hallamlab · Apr 17, 2023 · 19e8366 · 19e8366
1 parent 42b7724
commit 19e8366
Show file tree

Hide file tree

Showing 7 changed files with 0 additions and 7 deletions.
diff --git a/high_throughput_screening/fabfos/lib/definition.py b/high_throughput_screening/fabfos/lib/definition.py
@@ -125,7 +125,6 @@ def procedure(context: JobContext) -> JobResult:
     """)
 
     return JobResult(
-        exit_code = 0,
         manifest = {
             ASSEMBLY: contigs,
             COVERAGE: str(cov),

diff --git a/high_throughput_screening/fosmid_walk/lib/definition.py b/high_throughput_screening/fosmid_walk/lib/definition.py
@@ -55,7 +55,6 @@ def procedure(context: JobContext) -> JobResult:
 
     sample_name = ".".join(reads.name.split(".")[:-1])
     return JobResult(
-        exit_code =code,
         manifest = {
             FW_FULL: context.output_folder.joinpath(f"{sample_name}_original.fasta"),
             FW_HITS: context.output_folder.joinpath(f"{sample_name}_hits.fasta"),

diff --git a/logistics/extract_mg-reads/lib/definition.py b/logistics/extract_mg-reads/lib/definition.py
@@ -81,7 +81,6 @@ def rm_file_extension(s: str):
     """)
 
     return JobResult(
-        exit_code = code,
         manifest = manifest,
     )
 

diff --git a/metagenomics/annotation_metapathways/lib/definition.py b/metagenomics/annotation_metapathways/lib/definition.py
@@ -65,7 +65,6 @@ def example_procedure(context: JobContext) -> JobResult:
         code = max(1, _code+code)
 
     return JobResult(
-        exit_code = code,
         manifest = {
             MP3_WS: out_folder,
             ANNOTATIONS: annotations,

diff --git a/metagenomics/checkm_on_bin/lib/definition.py b/metagenomics/checkm_on_bin/lib/definition.py
@@ -48,7 +48,6 @@ def _procedure(context: JobContext) -> JobResult:
     """)
 
     return JobResult(
-        exit_code = code,
         manifest = {
             CHECKM_WS: out_folder,
             CHECKM_STATS: out_stats,

diff --git a/metagenomics/metagenomic_assembly/lib/definition.py b/metagenomics/metagenomic_assembly/lib/definition.py
@@ -95,7 +95,6 @@ def _megahit(reads: list[Path]):
     """)
 
     return JobResult(
-        exit_code = code,
         manifest = {
             ASM: out,
             ASM_WS: ws

diff --git a/metagenomics/taxonomy_on_bin/lib/gtdbtk.py b/metagenomics/taxonomy_on_bin/lib/gtdbtk.py
@@ -80,7 +80,6 @@ def gtdbtk_procedure(context: JobContext, SAMPLE, BINS, GTDBTK_WS, GTDBTK_TAX, C
     """)
 
     return JobResult(
-        exit_code = code,
         manifest = {
             GTDBTK_WS: out_folder,
             GTDBTK_TAX: summary,
-Original file line number
+Diff line change
@@ Expand Up / @@ -81,7 +81,6 @@ def rm_file_extension(s: str): @@
         """)
         return JobResult(
-            exit_code = code,
             manifest = manifest,
         )
@@ Expand Down @@