diff --git a/rna-seq.nf b/rna-seq.nf index 305106d3ae1cf0d6d4655d5db94959199641f075..b273f869a09afeec86a34249a8db3f290b36e25a 100644 --- a/rna-seq.nf +++ b/rna-seq.nf @@ -812,7 +812,7 @@ process seqwho { echo -e "LOG: concordant species inference: \${speciesInfer}" >> ${repRID}.seqwho.log else speciesErrorSeqwho=true - speciesErrorSeqwho_details="**inferred species does not match for R1 and R2:** inferred R1 = \${speciesR1} and inferred R2 = \${speciesR2}" + speciesErrorSeqwho_details="**Inferred species does not match for R1 and R2:** Inferred R1 = \${speciesR1} and inferred R2 = \${speciesR2}" echo -e "LOG: inference error: \${speciesErrorSeqwho_details}" >> ${repRID}.seqwho.log fi @@ -822,8 +822,8 @@ process seqwho { echo -e "LOG: high confidence species inference detected" >> ${repRID}.seqwho.log else speciesErrorSeqwho=true - speciesErrorSeqwho_details=\$(echo "**inferred species confidence is low:**\\n") - speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|fastq|inferred species confidence|\\n") + speciesErrorSeqwho_details=\$(echo "**Inferred species confidence is low:**\\n") + speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|fastq|Inferred species confidence|\\n") speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|:--|:--:|\\n") speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|Read 1|\${speciesConfidenceR1}|\\n") if [ "${ends}" == "pe" ] @@ -846,12 +846,12 @@ process seqwho { echo -e "LOG: concordant rnaseq seq type inference detected" >> ${repRID}.seqwho.log else seqtypeError=true - seqtypeError_details="**inferred sequencing type is not mRNA-seq:** inferred = \${seqtypeR1}" + seqtypeError_details="**Inferred sequencing type is not mRNA-seq:** Inferred = \${seqtypeR1}" echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log fi else seqtypeError=true - seqtypeError_details="**inferred sequencing type does not match for R1 and R2:** inferred R1 = \${seqtypeR1} and inferred R2 = \${seqtypeR2}" + seqtypeError_details="**Inferred sequencing type does not match for R1 and R2:** Inferred R1 = \${seqtypeR1} and inferred R2 = \${seqtypeR2}" echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log fi consensus="-" @@ -901,8 +901,8 @@ process seqwho { if [ \${consensus} == false ] then seqtypeError=true - seqtypeError_details=\$(echo "**inferred sequence-type confidence is low:**\\n") - seqtypeError_details=\$(echo \${seqtypeError_details}"|fastq|inferred seq type|inferred seq type confidence|\\n") + seqtypeError_details=\$(echo "**Inferred sequence-type confidence is low:**\\n") + seqtypeError_details=\$(echo \${seqtypeError_details}"|fastq|Inferred seq type|Inferred seq type confidence|\\n") seqtypeError_details=\$(echo \${seqtypeError_details}"|:--|:--:|:--:|\\n") seqtypeError_details=\$(echo \${seqtypeError_details}"|Read 1|\${seqtypeR1}|\${seqtypeConfidenceR1}|\\n") if [ "${ends}" == "pe" ]