tcoffee sp100 + t 30

Snakefile

@@ -31,7 +31,7 @@ READS_ILLUMINA_BMB="ERR1308675.fastq"
 REF_CCN="ccnscafold.fa"
 REF_BMB="bmbscafold.fa"
 ID=["CCN_yeast","BMB_yeast","diploid_yeast","ecoli_hifi","ecoli_illumina","human"]
-CONFIGS=["_sp10","_clustal","_tcoffee","_sp100"]
+CONFIGS=["_sp10","_clustal","_tcoffee","_sp100","_tcoffee_sp100"]
 
 READS_HUMAN="reads.fastq"
 REF_HUMAN="chm13.draft_v1.1.fasta"
@@ -874,7 +874,7 @@ rule configuration_files_sp10:
         'tail -2 {input} >>{output};'
         'echo -e "D: [10,20,30,45,50,60,100,150,200]" >>{output};'
         'echo -e "S: [100,200,500,1000,2000,5000,10000]" >>{output};'
-        'echo -e "T: [50,60,70,80]" >>{output};'
+        'echo -e "T: [30,50,60,70,80]" >>{output};'
         'echo -e "M: [muscle,mafft,poa,spoa,abpoa,kalign,kalign3]" >>{output};'
         'echo -e "O: 10" >>{output}'
         
@@ -894,7 +894,7 @@ rule configuration_files_for_clustal:
         'tail -2 {input} >>{output};'
         'echo -e "D: [10,20,30,45,50,60,100,150,200]" >>{output};'
         'echo -e "S: [100,200,500,1000,2000,5000,10000]" >>{output};'
-        'echo -e "T: [50,60,70,80]" >>{output};'
+        'echo -e "T: [30,50,60,70,80]" >>{output};'
         'echo -e "M: [clustalo]" >>{output};'
         'echo -e "O: 10" >>{output}'
 
@@ -914,7 +914,7 @@ rule configuration_files_for_tcoffee:
         'tail -2 {input.config} >>{output};'
         'echo -e "D: [10,20,30,45,50,60,100]" >>{output};'
         'echo -e "S: [100,200,500,1000]" >>{output};'
-        'echo -e "T: [50,60,70,80]" >>{output};'
+        'echo -e "T: [30,50,60,70,80]" >>{output};'
         'echo -e "M: [tcoffee]" >>{output};'
         'echo -e "B: [`cat {input.start}`]" >>{output}'
         
@@ -933,6 +933,25 @@ rule configuration_files_for_sp100:
         'tail -2 {input} >>{output};'
         'echo -e "D: [10,20,30,45,50,60,100,150,200]" >>{output};'
         'echo -e "S: [500]" >>{output};'
-        'echo -e "T: [50,60,70,80]" >>{output};'
+        'echo -e "T: [30,50,60,70,80]" >>{output};'
         'echo -e "M: [muscle,mafft,poa,spoa,abpoa,kalign,kalign3]" >>{output};'
         'echo -e "O: 100" >>{output}'
+
+rule configuration_files_for_sp100_tcoffee:
+    input :
+        os.path.join('before_configuration_files','config_{id}.yaml'),
+    output :
+        os.path.join('configuration_files','config_tcoffee_sp100_{id}.yaml')
+    message :
+        "Configuration files for sp100 tcoffee ({wildcards.id})"
+    log:
+        os.path.join('logs','configuration_files','3_configuration_files_for_tcoffee_sp100_{id}.log')
+    shell:
+        'set +o pipefail;'
+        'head -1 {input}| sed "s/$/_sp100_tcoffee/" >{output};'
+        'tail -2 {input} >>{output};'
+        'echo -e "D: [10,20,30,45,50,60,100,150,200]" >>{output};'
+        'echo -e "S: [500]" >>{output};'
+        'echo -e "T: [30,50,60,70,80]" >>{output};'
+        'echo -e "M: [tcoffee]" >>{output};'
+        'echo -e "O: 100" >>{output}'