Merge pull request #134 from GlobalPneumoSeq/dev

Release Version 1.0.0-rc11

bin/generate_overall_report.py

@@ -33,8 +33,8 @@
 
 
 def main():
-    ariba_targets = set(pd.read_csv(ARIBA_METADATA, sep='\t')['target'].unique())
-    df_resistance_to_mic = pd.read_csv(RESISTANCE_TO_MIC, sep='\t', index_col='drug')
+    ariba_targets = set(pd.read_csv(ARIBA_METADATA, sep='\t', keep_default_na=False)['target'].unique())
+    df_resistance_to_mic = pd.read_csv(RESISTANCE_TO_MIC, sep='\t', index_col='drug', keep_default_na=False)
 
     output_columns = get_output_columns(COLUMNS_BY_CATEGORY, ariba_targets)
     df_output = get_df_output(INPUT_PATTERN, output_columns, df_resistance_to_mic)
@@ -82,7 +82,7 @@ def get_df_output(input_pattern, output_columns, df_resistance_to_mic):
     dfs = [df_manifest]
     reports = glob.glob(input_pattern)
     for report in reports:
-        df = pd.read_csv(report, dtype=str)
+        df = pd.read_csv(report, dtype=str, keep_default_na=False)
         dfs.append(df)
     df_output = pd.concat(dfs, ignore_index=True).sort_values(by=['Sample_ID'])
 
@@ -91,6 +91,9 @@ def get_df_output(input_pattern, output_columns, df_resistance_to_mic):
 
     df_output = add_inferred_mic(df_output, df_resistance_to_mic)
 
+    # Missing in silico results in Overall QC pass samples means failure in corresponding typing module
+    df_output.loc[df_output["Overall_QC"] == "PASS"] = df_output.loc[df_output["Overall_QC"] == "PASS"].fillna(value="MODULE FAILURE")
+
     return df_output
 
 #  Add inferred MIC (minimum inhibitory concentration) based on resistance phenotypes if the drug exists in the lookup table
@@ -102,7 +105,7 @@ def add_inferred_mic(df_output, df_resistance_to_mic):
 
         if res_col_name in df_output:
             res_col_index = df_output.columns.get_loc(res_col_name)
-            mic_series = df_output[res_col_name].map(resistance_to_mic, na_action='ignore')
+            mic_series = df_output[res_col_name].map(resistance_to_mic, na_action='ignore').fillna(value="_")
             df_output.insert(res_col_index, f'{drug}_MIC', mic_series)
 
     return df_output

bin/get_overall_qc.sh

@@ -1,16 +1,55 @@
 # Determine overall QC result based on File Validity, Read QC, Assembly QC, Mapping QC and Taxonomy QC
 # In case File Validity is not PASS, save its value (i.e. description of the issue) to Overall QC
-# In case of assembler failure, there will be no Assembly QC input, save ASSEMBLER FAILURE to Overall QC
-
-if [[ ! "$FILE_VALIDITY" == "PASS" ]]; then
-    OVERALL_QC="$FILE_VALIDITY"
-elif [[ "$READ_QC" == "PASS" ]] && [[ "$ASSEMBLY_QC" == "PASS" ]] && [[ "$MAPPING_QC" == "PASS" ]] && [[ "$TAXONOMY_QC" == "PASS" ]]; then
-    OVERALL_QC="PASS"
-elif [[ "$READ_QC" == "PASS" ]] && [[ "$ASSEMBLY_QC" == "null" ]]; then
-    OVERALL_QC="ASSEMBLER FAILURE"
-else
-    OVERALL_QC="FAIL"
-fi
+# In case of preprocess/assembly/mapping/taxonomy failure, there will be no relevant QC input, save corresponding MODULE FAILURE to Overall QC
+
+assign_overall_qc() {
+    if [[ "$FILE_VALIDITY" == "null" ]]; then
+        OVERALL_QC="FILE VALIDATION FAILURE"
+        return
+    fi
+
+    if [[ ! "$FILE_VALIDITY" == "PASS" ]]; then
+        OVERALL_QC="$FILE_VALIDITY"
+        return
+    fi
+
+    if [[ "$READ_QC" == "null" ]]; then
+        OVERALL_QC="PREPROCESS MODULE FAILURE"
+        return
+    fi 
+
+    if [[ "$READ_QC" == "FAIL" ]]; then
+        OVERALL_QC="FAIL"
+        return
+    fi 
+
+    OVERALL_QC=""
+
+    if [[ "$ASSEMBLY_QC" == "null" ]]; then
+        OVERALL_QC+="ASSEMBLY MODULE FAILURE;"
+    fi
+
+    if [[ "$MAPPING_QC" == "null" ]]; then
+        OVERALL_QC+="MAPPING MODULE FAILURE;"
+    fi
+
+    if [[ "$TAXONOMY_QC" == "null" ]]; then
+        OVERALL_QC+="TAXONOMY MODULE FAILURE;"
+    fi
+
+    if [[ ! "$OVERALL_QC" == "" ]]; then
+        OVERALL_QC="${OVERALL_QC%;}"
+        return
+    fi
+
+    if [[ "$READ_QC" == "PASS" ]] && [[ "$ASSEMBLY_QC" == "PASS" ]] && [[ "$MAPPING_QC" == "PASS" ]] && [[ "$TAXONOMY_QC" == "PASS" ]]; then
+        OVERALL_QC="PASS"
+    else
+        OVERALL_QC="FAIL"
+    fi
+}
+
+assign_overall_qc
 
 echo \"Overall_QC\" > "$OVERALL_QC_REPORT"
 echo \""$OVERALL_QC"\" >> "$OVERALL_QC_REPORT"

bin/get_serotype.sh

@@ -1,10 +1,6 @@
 # Run SeroBA to serotype samples
 
-{
-    seroba runSerotyping "${SEROBA_DB}" "$READ1" "$READ2" "$SAMPLE_ID" && SEROTYPE=$(awk -F'\t' '{ print $2 }' "${SAMPLE_ID}/pred.tsv")
-} || {
-    SEROTYPE="SEROBA FAILURE"
-}
+seroba runSerotyping "${SEROBA_DB}" "$READ1" "$READ2" "$SAMPLE_ID" && SEROTYPE=$(awk -F'\t' '{ print $2 }' "${SAMPLE_ID}/pred.tsv")
 
 echo \"Serotype\" > "$SEROTYPE_REPORT"
 echo \""$SEROTYPE"\" >> "$SEROTYPE_REPORT"

bin/parse_other_resistance.py

@@ -31,7 +31,7 @@ def main():
 
 # Saving all targets in metadata as key and their information as values
 def get_target():
-    df_metadata = pd.read_csv(METADATA_PATH, sep='\t')
+    df_metadata = pd.read_csv(METADATA_PATH, sep='\t', keep_default_na=False)
     target_dict = defaultdict(lambda: defaultdict(set))
 
     # Add ref_group based on ref_name to the Dataframe
@@ -71,7 +71,7 @@ def get_target():
 
 # Finding hits in ARIBA results based on targets_dict and save hits to hits_dict
 def find_hit(target_dict):
-    df_report = pd.read_csv(DEBUG_REPORT_PATH, sep="\t")
+    df_report = pd.read_csv(DEBUG_REPORT_PATH, sep="\t", keep_default_na=False)
 
     # Remove rows with non-numeric value in ref_base_assembled, ref_len, or ctg_cov
     df_report['ref_base_assembled'] = pd.to_numeric(df_report['ref_base_assembled'], errors='coerce')

bin/parse_pbp_resistance.sh

@@ -1,35 +1,30 @@
 # Extract the results from the output file of the PBP AMR predictor
 
-# For all, replace null or space-only string with empty string
+# For all, replace null, empty, or space-only string with underscore
 
 function GET_VALUE {
     < "$JSON_FILE" jq -r --arg target "$1" '.[$target]' \
-        | sed 's/^null$//g;s/^\s+$//g'
-}
-
-function GET_RES {
-    < "$JSON_FILE" jq -r --arg target "$1" '.[$target]' \
-        | sed 's/^null$//g;s/^\s+$//g'
+        | sed 's/^\(null\|\s*\)$/_/g'
 }
 
 pbp1a=$(GET_VALUE "pbp1a")
 pbp2b=$(GET_VALUE "pbp2b")
 pbp2x=$(GET_VALUE "pbp2x")
 AMO_MIC=$(GET_VALUE "amxMic")
-AMO=$(GET_RES "amx")
+AMO=$(GET_VALUE "amx")
 CFT_MIC=$(GET_VALUE "croMic")
-CFT_NONMENINGITIS=$(GET_RES "croNonMeningitis")
-CFT_MENINGITIS=$(GET_RES "croMeningitis")
+CFT_NONMENINGITIS=$(GET_VALUE "croNonMeningitis")
+CFT_MENINGITIS=$(GET_VALUE "croMeningitis")
 TAX_MIC=$(GET_VALUE "ctxMic")
-TAX_NONMENINGITIS=$(GET_RES "ctxNonMeningitis")
-TAX_MENINGITIS=$(GET_RES "ctxMeningitis")
+TAX_NONMENINGITIS=$(GET_VALUE "ctxNonMeningitis")
+TAX_MENINGITIS=$(GET_VALUE "ctxMeningitis")
 CFX_MIC=$(GET_VALUE "cxmMic")
-CFX=$(GET_RES "cxm")
+CFX=$(GET_VALUE "cxm")
 MER_MIC=$(GET_VALUE "memMic")
-MER=$(GET_RES "mem")
+MER=$(GET_VALUE "mem")
 PEN_MIC=$(GET_VALUE "penMic")
-PEN_NONMENINGITIS=$(GET_RES "penNonMeningitis")
-PEN_MENINGITIS=$(GET_RES "penMeningitis")
+PEN_NONMENINGITIS=$(GET_VALUE "penNonMeningitis")
+PEN_MENINGITIS=$(GET_VALUE "penMeningitis")
 
 echo \"pbp1a\",\"pbp2b\",\"pbp2x\",\"AMO_MIC\",\"AMO_Res\",\"CFT_MIC\",\"CFT_Res\(Meningital\)\",\"CFT_Res\(Non-meningital\)\",\"TAX_MIC\",\"TAX_Res\(Meningital\)\",\"TAX_Res\(Non-meningital\)\",\"CFX_MIC\",\"CFX_Res\",\"MER_MIC\",\"MER_Res\",\"PEN_MIC\",\"PEN_Res\(Meningital\)\",\"PEN_Res\(Non-meningital\)\" > "$PBP_AMR_REPORT"
 echo \""$pbp1a"\",\""$pbp2b"\",\""$pbp2x"\",\""$AMO_MIC"\",\""$AMO"\",\""$CFT_MIC"\",\""$CFT_MENINGITIS"\",\""$CFT_NONMENINGITIS"\",\""$TAX_MIC"\",\""$TAX_MENINGITIS"\",\""$TAX_NONMENINGITIS"\",\""$CFX_MIC"\",\""$CFX"\",\""$MER_MIC"\",\""$MER"\",\""$PEN_MIC"\",\""$PEN_MENINGITIS"\",\""$PEN_NONMENINGITIS"\" >> "$PBP_AMR_REPORT"

data/ariba_metadata.tsv

@@ -32,7 +32,7 @@ parE_AE007317	1	1	D435H	.	FQ
 parE_AE007317	1	1	D435N	.	FQ
 parE_AE007317	1	1	E474K	.	FQ
 parE_AE007317	1	1	P454S	.	FQ
-aph_3prime_III_1_M26832	1	0	.	.	KAN
+aph3primeIII_1_M26832	1	0	.	.	KAN
 rpoB_AE007317	1	1	D489E	.	RIF
 rpoB_AE007317	1	1	D489N	.	RIF
 rpoB_AE007317	1	1	H499N	.	RIF
@@ -59,10 +59,10 @@ tetM_MH283017	1	0	.	.	TET
 tetO_Y07780	1	0	.	.	TET
 tetS_FN555436	1	0	.	.	TET
 tetS_FN555436	1	0	.	.	TET
-tetS_M	1	0	.	.	TET
-tetS_M_AY534326	1	0	.	.	TET
-tetS_M_HM367711	1	0	.	.	TET
-tetS_M_MH283012	1	0	.	.	TET
+tetSM	1	0	.	.	TET
+tetSM_AY534326	1	0	.	.	TET
+tetSM_HM367711	1	0	.	.	TET
+tetSM_MH283012	1	0	.	.	TET
 tetT_L42544	1	0	.	.	TET
 tetW_AJ222769	1	0	.	.	TET
 folA_2_29594_2_181	1	1	I100L	.	TMP

data/ariba_ref_sequences.fasta

@@ -1,4 +1,4 @@
->aph_3prime_III_1_M26832
+>aph3primeIII_1_M26832
 ATGGCTAAAATGAGAATATCACCGGAATTGAAAAAACTGATCGAAAAATACCGCTGCGTAAAAGATACGGAAGGAATGTCTCCTGCTAAGGTATATAAGCTGGTGGGAGAAAATGAAAACCTATATTTAAAAATGACGGACAGCCGGTATAAAGGGACCACCTATGATGTGGAACGGGAAAAGGACATGATGCTATGGCTGGAAGGAAAGCTGCCTGTTCCAAAGGTCCTGCACTTTGAACGGCATGATGGCTGGAGCAATCTGCTCATGAGTGAGGCCGATGGCGTCCTTTGCTCGGAAGAGTATGAAGATGAACAAAGCCCTGAAAAGATTATCGAGCTGTATGCGGAGTGCATCAGGCTCTTTCACTCCATCGACATATCGGATTGTCCCTATACGAATAGCTTAGACAGCCGCTTAGCCGAATTGGATTACTTACTGAATAACGATCTGGCCGATGTGGATTGCGAAAACTGGGAAGAAGACACTCCATTTAAAGATCCGCGCGAGCTGTATGATTTTTTAAAGACGGAAAAGCCCGAAGAGGAACTTGTCTTTTCCCACGGCGACCTGGGAGACAGCAACATCTTTGTGAAAGATGGCAAAGTAAGTGGCTTTATTGATCTTGGGAGAAGCGGCAGGGCGGACAAGTGGTATGACATTGCCTTCTGCGTCCGGTCGATCAGGGAGGATATCGGGGAAGAACAGTATGTCGAGCTATTTTTTGACTTACTGGGGATCAAGCCTGATTGGGAGAAAATAAAATATTATATTTTACTGGATGAATTGTTTTAG
 >ermB_1_JN899585
 ATGAACAAAAATATAAAATATTCTCAAAACTTTTTAACGAGTGAAAAAGTACTCAACCAAATAATAAAACAATTGAATTTAAAAGAAACCGATACCGTTTACGAAATTGGAACAGGTAAAGGGCATTTAACGACGAAACTGGCTAAAATAAGTAAACAGGTAACGTCTATTGAATTAGACAGTCATCTATTCAACTTATCGTCAGAAAAATTAAAACTGAATACTCGTGTCACTTTAATTCACCAAGATATTCTACAGTTTCAATTCCCTAACAAACAGAGGTATAAAATTGTTGGGAATATTCCTTACCATTTAAGCACACAAATTATTAAAAAAGTGGTTTTTGAAAGCCATGCGTCTGACATCTATCTGATTGTTGAAGAAGGATTCTACAAGCGTACCTTGGATATTCACCGAACACTAGGGTTGCTCTTGCACACTCAAGTCTCGATTCAGCAATTGCTTAAGCTGCCAGCGGAATGCTTTCATCCTAAACCAAAAGTAAACAGTGTCTTAATAAAACTTACCCGCCATACCACAGATGTTCCAGATAAATATTGGAAGCTATATACGTACTTTGTTTCAAAATGGGTCAATCGAGAATATCGTCAACTGTTTACTAAAAATCAGTTTCATCAAGCAATGAAACACGCCAAAGTAAACAATTTAAGTACCGTTACTTATGAGCAAGTATTGTCTATTTTTAATAGTTATCTATTATTTAACGGGAGGAAATAA
@@ -42,7 +42,7 @@ ATGAAAATTATTAATATTGGAGTTTTAGCTCATGTTGATGCAGGAAAAACTACCTTAACAGAAAGCTTATTATATAACAG
 ATGAAAATTATTAATATTGGAGTTTTAGCTCATGTTGATGCAGGAAAAACTACCTTAACAGAAAGCTTATTATATAACAGTGGAGCGATTACAGAATTAGGAAGCGTGGACAAAGGTACAACGAGGACGGATAATACGCTTTTAGAACGTCAGAGAGGAATTACAATTCAGACAGGAATAACCTCTTTTCAGTGGGAAAATACGAAGGTGAACATCATAGACACGCCAGGACATATGGATTTCTTAGCAGAAGTATATCGTTCATTATCAGTTTTAGATGGGGCAATTCTACTGATTTCTGCAAAAGATGGCGTACAAGCACAAACTCGTATATTATTTCATGCACTTAGGAAAATGGGGATTCCCACAATCTTTTTTATCAATAAGATTGACCAAAATGGAATTGATTTATCAACGGTTTATCAGGATATTAAAGAGAAACTTTCTGCCGAAATTGTAATCAAACAGAAGGTAGAACTGTATCCTAATATGTGTGTGACGAACTTTACCGAATCTGAACAATGGGATACGGTAATAGAGGGAAACGATGACCTTTTAGAGAAATATATGTCCGGTAAATCATTAGAAGCATTGGAACTCGAACAAGAGGAAAGCATAAGATTTCAGAATTGTTCTCTGTTCCCTCTTTATCATGGAAGTGCAAAAAGTAATATAGGGATTGATAACCTTATAGAAGTTATTACTAATAAATTTTATTCATCAACACATCGAGGTCCGTCTGAACTTTGCGGAAATGTTTTCAAAATTGAATATACAAAAAAAAGACAACGTCTTGCATATATACGTCTTTATAGTGGAGTACTACATTTACGAGATTCGGTTAGAATATCGGAAAAGGAAAAAATAAAAATTACAGAAATGTATACTTCAATAAATGGTGAATTATGTAAAATCGATAAGGCTTATTCTGGAGAAATTGTTATTTTGCAAAATGAGTTTTTGAAGTTAAATAGTGTTCTTGGAGATACAAAACTATTGCCACAGAGAAAAAGAATTGAAAATCCGCACCCTCTACTACAAACAACTGTTGAACCGAGTAAACCTGAACAGAGAGAAATGTTGCTTGATGCCCTTTTGGAAATCTCAGATAGTGATCCGCTTCTACGATATTACGTGGATTCTACGACACATGAAATTATACTTTCTTTCTTAGGGAAAGTACAAATGGAAGTGATTAGTGCACTGTTGCAAGAAAAGTATCATGTGGAGATAGAACTAAAAGAGCCTACAGTCATTTATATGGAGAGACCGTTAAAAAATGCAGAATATACCATTCACATCGAAGTGCCGCCAAATCCTTTCTGGGCTTCCATTGGTTTATCTGTATCACCGCTTCCGTTGGGAAGTGGAATGCAGTATGAGAGCTCGGTTTCTCTTGGATACTTAAATCAATCATTTCAAAATGCAGTTATGGAAGGGATACGCTATGGTTGCGAACAAGGATTATATGGTTGGAATGTGACGGACTGTAAAATCTGTTTTAAGTATGGCTTATACTATAGCCCTGTTAGTACCCCAGCAGATTTTCGGATGCTTGCTCCTATTGTATTGGAACAAGTCTTAAAAAAAGCTGGAACAGAATTGTTAGAGCCATATCTTAGTTTTAAAATTTATGCGCCACAGGAATATCTTTCACGAGCATACAACGATGCTCCTAAATATTGTGCGAACATCGTAGACACTCAATTGAAAAATAATGAGGTCATTCTTAGTGGAGAAATCCCTGCTCGGTGTATTCAAGAATATCGTAGTGATTTAACTTTCTTTACAAATGGACGTAGTGTTTGTTTAACAGAGTTAAAAGGGTACCATGTTACTACCGGTGAACCTGTTTGCCAGCCCCGTCGTCCAAATAGTCGGATAGATAAAGTACGATATATGTTCAATAAAATAACTTAG
 >tetM_8_X04388
 ATGAAAATTATTAATATTGGAGTTTTAGCTCATGTTGATGCGGGAAAAACTACCTTAACAGAAAGCTTATTATATAACAGTGGAGCGATTACAGAATTAGGAAGCGTGGACAGAGGTACAACGAAAACGGATAATACGCTTTTAGAACGTCAGAGAGGAATTACAATTCAGACGGCGATAACCTCTTTTCAGTGGAAAAATACTAAGGTGAACATCATAGACACGCCAGGACATATGGATTTTTTAGCAGAAGTATATCGTTCATTATCAGTATTAGATGGGGCAATTCTACTGATTTCTGCAAAAGATGGCGTACAAGCACAAACTCGTATATTGTTTCATGCACTTAGGAAAATAGGTATTCCCACAATCTTTTTTATCAATAAGATTGACCAAAATGGAATTGATTTATCAACGGTTTATCAGGATATTAAAGAGAAACTTTCTGCGGAAATTGTAATCAAACAGAAGGTAGAACTGCATCCTAATATGCGTGTAATGAACTTTACCGAATCTGAACAATGGGATATGGTAATAGAAGGAAATGATTACCTTTTGGAGAAATATACGTCTGGGAAATTATTGGAAGCATTAGAACTCGAACAAGAGGAAAGCATAAGATTTCATAATTGTTCCCTGTTCCCTGTTTATCACGGAAGTGCAAAAAACAATATAGGGATTGATAACCTTATAGAAGTGATTACGAATAAATTTTATTCATCAACACATCGAGGTCAGTCTGAACTTTGCGGAAAAGTTTTCAAAATTGAGTATTCGGAAAAAAGACAGCGTCTTGCATATATACGTCTTTATAGTGGCGTACTGCATTTGCGAGATCCGGTTAGAATATCGGAAAAGGAAAAAATAAAAATTACAGAAATGTATACTTCAATAAATGGTGAATTATGTAAAATCGATAAGGCTTATTCCGGGGAAATTGTTATTTTGCAGAATGAGTTTTTGAAGTTAAATAGTGTTCTTGGAGATACAAAGCTATTGCCACAGAGAGAGAGAATTGAAAATCCCCTCCCTCTGCTGCAAACGACTGTTGAACCGAGCAAACCTCAACAAAGGGAAATGTTACTTGATGCACTTTTAGAAATCTCCGACAGTGACCCGCTTCTGCGATATTATGTGGATTCTGCGACACATGAAATCATACTTTCTTTCTTAGGGAAAGTACAAATGGAAGTGACTTGTGCTCTGCTGCAAGAAAAGTATCATGTGGAGATAGAAATAAAAGAGCCTACAGTCATTTATATGGAAAGACCGTTAAAAAAAGCAGAGTATACCATTCACATCGAAGTTCCACCGAATCCTTTCTGGGCTTCCATTGGTCTATCTGTAGCACCGCTTCCATTAGGGAGCGGAGTACAGTATGAGAGCTCGGTTTCTCTTGGATACTTAAATCAATCGTTTCAAAATGCAGTTATGGAGGGGATACGCTATGGCTGTGAACAAGGATTGTATGGTTGGAATGTGACGGACTGTAAAATCTGTTTTAAGTATGGCTTATACTATAGCCCTGTTAGTACCCCAGCAGATTTTCGGATGCTTGCTCCTATTGTATTGGAACAAGTCTTAAAAAAAGCTGGAACAGAATTGTTAGAGCCATATCTTAGTTTTAAAATTTATGCGCCACAGGAATATCTTTCACGAGCATACAACGATGCTCCTAAATATTGTGCGAACATCGTAGACACTCAATTGAAAAATAATGAGGTCATTCTTAGTGGAGAAATCCCTGCTCGGTGTATTCAAGAATATCGTAGTGATTTAACTTTCTTTACAAATGGACGTAGTGTTTGTTTAACAGAGTTAAAAGGGTACCATGTTACTACCGGTGAACCTGTTTGCCAGCCCCGTCGTCCAAATAGTCGGATAGATAAAGTACGATATATGTTCAATAAAATAACTTAG
->tetS_M
+>tetSM
 ATGGAGGAAATAAAATTGAAAATTATTAATATCGGTATCTTAGCACATGTTGATGCAGGAAAAACTACTTTGACAGAAAGCTTACTATACAGTAGCGGAGCAATTAAAGAGTTAGGAAGTGTAGATAGCGGTACAACGAAAACGGATACTATGTTTTTGGAACGCCAGAGAGGTATTACTATTCAGACCGCAATAACATCTTTTCAACGGGAAAATGTTAAAGTAAATATTGTAGATACTCCTGGACACATGGATTTTTTGGCAGATGTATACCGTTCATTATCTGTTTTGGATGGAGCTATTTTGCTAATCTCTGCAAAAGATGGAGTACAGTCACAAACTCGTATACTATTCCATGCACTTAGAAAGATGAACATACCTATAATATTTTTTATTAACAAAATTGATCAAAATGGAATAAATTTGCCAGATGTTTATCAAGATATTAAGGACAAACTTTCTGACGACATCATAATTAAGCAGACTGTGAATCTAAATTTGAAACCTTATGTAATAGATTATACTGAACCAGAACAATGGGAGACAGTAATTGTGGGAAATGATTATTTATTAGAAAAATATACCATTGGGAAAACATTGAATATTGCAGAACTTGAAAAGGAGGAAAACGAAAGAATTCAAAGTTGCTCCTTATATCCTGTTTATCACGGAAGTGCAAAGAATAATATTGGAATTAAACAACTTATAGAGGTAATTACTAGCAAATTATTTTCACCCACACAACTCAATTCAGATAAACTTTGTGGAAATGTTTTTAAAGTAGAATATTCAGATGATGGTCAACGGCTTGTCTATGTACGTCTTTATAGTGGAACGCTACATTTGCGAGACTCAGTCAATATATCAGAAAAGGAAAAAATAAAAGTTACAGAAATGTATACTTCAATAAATGGAGAATTACGCCAGATAGATAAGGCAGAGCCTGGTGAGATTATTATTTTAAAAAATGAGCTTTTAAAACTAAATAACGTACTTGGAGATAAAAAAAGATTACCACATAGAGAAATTCTTGAGAATCCTCTTCCTATGTTACAAACAACAATTGAACCATGTAAATCAGTACAAAGAGAAAAGTTACTAGATGCACTTTTTGAAATATCCGATAGTGATCCCCTTCTACAATATTATGTAGATACAGTAACTCACGAAATTGTGCTATCTTTTTTAGGTGAGGTCCAAATGGAGGTAACTTGTACTCTGATTCAAGAAAAATATCATATTGAGATAGAAACAAGAAAACCAACTGTCATTTATATGGAAAGACCATTAAAAAAATCTGAATTTACCATTGATATCGAAGTACCTCCAAATCCTTTCTGGGCTTCTATTGGTTTATCTGTAACACCACTTCCTTTGGGTAGTGGCATTCAGTATGAGAGCCTGGTTTCTCTAGGTTATTTAAATCAATCATTTCAAAATGCAGTTATGGAAGGTATACGCTATGGGTGTGAACAAGGATTGTACGGTTGGAAATTAACAGACTGTAAGATCTGTTTTAAGTATGGTCTATATTACAGCCCTGTCAGTACGCCAGCAGATTTCCGAATGCTTGCGCCTATTGTACTAGAGCAGGCTTTTAGAAAGAGTGGTACAGAGTTATTAGAGCCATATCTTAGCTTCGAAATTTATGTACCACAAGAATATCTTTCGAGAGCATATAATGATGCTTCCAAATATTGTGCAAATATTTTAAATACTAAGTTAAAAGGTAACGAGGTCATTCTCATTGGTGAAATTCCAGCCCGTTGTATTCAAGAGTATCAAAACAGTTTAACTTTCTTTACAAATGGACGCAGTGTCTGTTTAACAGAGTTAAAAGGGTACCATGTTACTACCGGTGAACCTGTTTGCCAGCCCCGTCGTCCAAATAGTCGGATAGATAAAGTACGATATATGTTCAATAAAATAACTTAG
 >tetO_Y07780
 ATGAAAATAATTAACTTAGGCATTCTGGCTCACGTTGACGCAGGAAAGACAACATTAACGGAGAGTTTAT
@@ -295,7 +295,7 @@ ATATACACTTAAATCTTCAAAGATATATATGCCTGCAAGGATTGATGCTGAAGCAGAAAAACGGATACAA
 GAAACGGCTGTAACTATATATAAAGCTCTGGGCTGTTCGGGTTTTTCCAGAGTGGATATGTTTTATACAC
 CGTCTGGCGAAATTGTATTTAATGAGGTAAACACAATACCAGGCTTTACCTCGCACAGTCGCTATCCAAA
 TATGATGAAAGGCATTGGTCTATCGTTCGCCCAAATGTTGGATAAGCTGATAGGTCTGTATGTGGAATGA
->tetS_M_MH283012
+>tetSM_MH283012
 TTGAAAATTATTAATATCGGTATCTTAGCACATGTTGATGCAGGAAAAACTACTTTGACAGAAAGCTTAC
 TATACAGTAGCGGAGCAATTAAAGAGTTAGGAAGTGTAGATAGCGGTACAACGAAAACGGATACTATGTT
 TTTGGAACGCCAGAGAGGTATTACTATTCAGACCGCAATAACATCTTTTCAACGGGAAAATGTTAAAGTA
@@ -686,7 +686,7 @@ GCCGCCGTGACGGCCCTGCTGGCCTCGCTGGGCGCGGACTTCACCGGAACGACGGGGGGCGACCCGGCCT
 GGATCGTCACCGGCGAGCTGCCGGCCCGGCGGGTGCGGGAGGCCGAGCTGCGGCTGCCGGGGCTGACGCA
 CGGGGAGGCGGTCTGGTCCTCCCGCCCTTGCGAGGACCGACCGCTGAAGGCCGGAAACTCTGGGCCTGGC
 ACGGGAGTTGGCGGGCATTCGGGTGAGTAG
->tetS_M_AY534326
+>tetSM_AY534326
 ATGGAGGAAATAAAATTGAAAATTATTAATATCGGTATCTTAGCACATGTTGATGCAGGAAAAACTACTT
 TGACAGAAAGCTTACTATACAGTAGCGGAGCAATTAAAGAGTTAGGAAGTGTAGATAGCGGTACAACGAA
 AACGGATACTATGTTTTTGGAACGCCAGAGAGGTATTACTATTCAGACCGCAATAACATCTTTTCAACGG
@@ -715,7 +715,7 @@ AATGATGCTTCCAAATATTGTGCAAATATTTTAAATACTAAGTTAAAAGGTAACGAGGTCATTCTCATTG
 GTGAAATCCCTGCTCGGTGTATTCAAGAATATCGTAGTGATTTAACTTTCTTTACAAATGGACGTAGTGT
 TTGTTTAACAGAGTTAAAAGGGTACCATGTTACTACCGGTGAACCTGTTTGCCAGCCCCGTCGTCCAAAT
 AGTCGGATAGATAAAGTACGATATATGTTCAATAAAATAACTTAG
->tetS_M_HM367711
+>tetSM_HM367711
 CTAAGTTATTTTATTGAACATATATCGTACTTTATCTATCCGACTATTTGGACGACGGGGCTGGCAAACA
 GGTTCACCGGTAGTAACATGGTACCCTTTTAACTCTGTTAAACAAACACTACGTCCATTTGTAAAGAAAG
 TTAAATCACTACGATATTCTTGAATACACCGATCAGGGATTTCTCCACTAAGAATGACCTCATTATTTTT

main.nf

@@ -1,7 +1,7 @@
 #!/usr/bin/env nextflow
 
 // Version of this release
-pipelineVersion = '1.0.0-rc10'
+pipelineVersion = '1.0.0-rc11'
 
 // Import workflow modules
 include { PIPELINE } from "$projectDir/workflows/pipeline"

modules/assembly.nf

@@ -2,9 +2,7 @@
 // Return sample_id and assembly, and publish the assembly to ${params.output}/assemblies directory based on ${params.assembly_publish}
 process ASSEMBLY_UNICYCLER {
     label 'unicycler_container'
-    label 'farm_high_fallible'
-
-    errorStrategy 'ignore'
+    label 'farm_high'
 
     tag "$sample_id"
 
@@ -37,9 +35,7 @@ process ASSEMBLY_UNICYCLER {
 // Return sample_id and assembly, and publish the assembly to ${params.output}/assemblies directory based on ${params.assembly_publish}
 process ASSEMBLY_SHOVILL {
     label 'shovill_container'
-    label 'farm_high_fallible'
-
-    errorStrategy 'ignore'
+    label 'farm_high'
 
     tag "$sample_id"
 

modules/info.nf

@@ -472,7 +472,7 @@ process FASTP_VERSION {
 
 process UNICYCLER_VERSION {
     label 'unicycler_container'
-    label 'farm_high_fallible'
+    label 'farm_high'
 
     output:
     tuple env(VERSION), env(THREAD)
@@ -486,7 +486,7 @@ process UNICYCLER_VERSION {
 
 process SHOVILL_VERSION {
     label 'shovill_container'
-    label 'farm_high_fallible'
+    label 'farm_high'
 
     output:
     tuple env(VERSION), env(THREAD)

modules/messages.nf

@@ -93,7 +93,7 @@ void endMessage(String selectedWorkflow) {
                 """.stripMargin()
             failMessage = '''
                 |The pipeline has failed.
-                |If you think it is caused by a bug, submit an issue at \"https://github.com/sanger-bentley-group/gps-pipeline/issues\".
+                |If you think it is caused by a bug, submit an issue at \"https://github.com/GlobalPneumoSeq/gps-pipeline/issues\".
                 '''.stripMargin()
             break
         case 'init':
@@ -112,7 +112,7 @@ void endMessage(String selectedWorkflow) {
                 '''.stripMargin()
             failMessage = '''
                 |Failed to get version information on pipeline, tools or databases.
-                |If you think it is caused by a bug, submit an issue at \"https://github.com/sanger-bentley-group/gps-pipeline/issues\"
+                |If you think it is caused by a bug, submit an issue at \"https://github.com/GlobalPneumoSeq/gps-pipeline/issues\"
                 '''.stripMargin()
             break
     }

modules/validate.nf

@@ -164,7 +164,7 @@ void validate(Map params) {
             default:
                 log.error("""
                     |Unknown value type \"${validParams[key]}\"
-                    |Please submit an issue at \"https://github.com/sanger-bentley-group/gps-pipeline/issues\"}
+                    |Please submit an issue at \"https://github.com/GlobalPneumoSeq/gps-pipeline/issues\"}
                     """.stripMargin())
                 System.exit(1)
         }