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Clinical-Genomics-Lund · May 8, 2024 · 4a59db8 · 4a59db8
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/configs/example.input.csv b/configs/example.input.csv
@@ -1,3 +1,3 @@
 clarity_sample_id,id,type,assay,group,bam,bai,purity
-CMD123456,Sample1,T,solid-pgx,Sample1,/fs1/results_dev/solid_hg38/bam/22PH00992-PGx-231020.T.bwa.umi.sort.bam,/fs1/results_dev/solid_hg38/bam/22PH00992-PGx-231020.T.bwa.umi.sort.bam.bai,0.30
-CMD987654,Sample2,T,solid-pgx,Sample2,/fs1/results_dev/solid_hg38/bam/21PH18790-PGx-231020.T.bwa.umi.sort.bam,/fs1/results_dev/solid_hg38/bam/21PH18790-PGx-231020.T.bwa.umi.sort.bam.bai,0.30
+XXXXXXX,Sample1,T,solid-pgx,Sample1,/path/to/Sample1.bam,/path/to/Sample1.bam.bai,0.30
+XXXXXXX,Sample2,T,solid-pgx,Sample2,/path/to/Sample2.bam,/path/to/Sample2.bam.bai,0.30
diff --git a/envs/get_cointainers.sh b/envs/get_cointainers.sh
@@ -10,5 +10,7 @@ sudo singularity build samtools.sif recepies/samtools
 sudo singularity build gatk3.sif docker://broadinstitute/gatk3:3.8-1
 sudo singularity build gatk4.sif docker://broadinstitute/gatk
 sudo singularity build bcftools.sif docker://staphb/bcftools
+sudo singularity build pharmcat.sif docker://pgkb/pharmcat
+
 
 
diff --git a/resources/templates/report.html b/resources/templates/report.html
@@ -116,7 +116,7 @@
       {% endfor %}
     {% else %}
       <tr>
-        <td colspan="4">Alla mål har läst djup mer än {{ read_depth }} (PGX_QC_PASS)</td>
+        <td colspan="4">Alla analyserade regioner har ett läsdjup på ≥ {{ read_depth }}x (PGX_QC_PASS)</td>
       </tr>
     {% endif %}
   </table>