nano commands.star
Put this in your commands file: apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b--h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C1_R1 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794483_C1_R1_1.fq ../data/GSM794483_C1_R1_2.fq apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b--h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C1_R2 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794484_C1_R2_1.fq ../data/GSM794484_C1_R2_2.fq apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b--h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C1_R3 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794485_C1_R3_1.fq ../data/GSM794485_C1_R3_2.fq apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b--h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C2_R1 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794486_C2_R1_1.fq ../data/GSM794486_C2_R1_2.fq apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b–h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C2_R2 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794487_C2_R2_1.fq ../data/GSM794487_C2_R2_2.fq apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b–h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C2_R3 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794488_C2_R3_1.fq ../data/GSM794488_C2_R3_2.fq |